From b8ddb0c12f6155b2de1a19d3b5f1fc2d158b69b2 Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Mon, 4 Apr 2011 13:13:54 +0200 Subject: [PATCH] Added 1 analysis tool manual. --- admin/programs.txt | 1 + man/man1/Makefile.am | 4 + man/man1/do_dssp.1 | 15 ++- man/man1/editconf.1 | 55 ++++---- man/man1/eneconv.1 | 14 +- man/man1/g_anadock.1 | 8 +- man/man1/g_anaeig.1 | 10 +- man/man1/g_analyze.1 | 46 +++---- man/man1/g_angle.1 | 22 ++-- man/man1/g_bar.1 | 109 +++++++++------ man/man1/g_bond.1 | 12 +- man/man1/g_bundle.1 | 12 +- man/man1/g_chi.1 | 75 +++++------ man/man1/g_cluster.1 | 20 +-- man/man1/g_clustsize.1 | 18 +-- man/man1/g_confrms.1 | 10 +- man/man1/g_covar.1 | 17 ++- man/man1/g_current.1 | 26 ++-- man/man1/g_density.1 | 22 ++-- man/man1/g_densmap.1 | 12 +- man/man1/g_dielectric.1 | 33 ++--- man/man1/g_dih.1 | 8 +- man/man1/g_dipoles.1 | 42 +++--- man/man1/g_disre.1 | 14 +- man/man1/g_dist.1 | 8 +- man/man1/g_dyndom.1 | 16 +-- man/man1/g_enemat.1 | 12 +- man/man1/g_energy.1 | 85 +++++------- man/man1/g_filter.1 | 14 +- man/man1/g_gyrate.1 | 16 +-- man/man1/g_h2order.1 | 14 +- man/man1/g_hbond.1 | 26 ++-- man/man1/g_helix.1 | 46 +++---- man/man1/g_helixorient.1 | 22 ++-- man/man1/g_lie.1 | 8 +- man/man1/g_mdmat.1 | 17 ++- man/man1/g_membed.1 | 51 ++++---- man/man1/g_mindist.1 | 8 +- man/man1/g_morph.1 | 18 +-- man/man1/g_msd.1 | 17 +-- man/man1/g_nmeig.1 | 50 ++++++- man/man1/g_nmens.1 | 6 +- man/man1/g_nmtraj.1 | 12 +- man/man1/g_order.1 | 16 +-- man/man1/g_polystat.1 | 8 +- man/man1/g_potential.1 | 12 +- man/man1/g_principal.1 | 8 +- man/man1/g_protonate.1 | 12 +- man/man1/g_rama.1 | 8 +- man/man1/g_rdf.1 | 30 ++--- man/man1/g_rms.1 | 24 ++-- man/man1/g_rmsdist.1 | 14 +- man/man1/g_rmsf.1 | 26 ++-- man/man1/g_rotacf.1 | 23 ++-- man/man1/g_rotmat.1 | 16 +-- man/man1/g_saltbr.1 | 17 +-- man/man1/g_sas.1 | 26 ++-- man/man1/g_select.1 | 8 +- man/man1/g_sgangle.1 | 20 +-- man/man1/g_sham.1 | 28 ++-- man/man1/g_sigeps.1 | 14 +- man/man1/g_sorient.1 | 24 ++-- man/man1/g_spatial.1 | 58 ++++---- man/man1/g_spol.1 | 10 +- man/man1/g_tcaf.1 | 40 +++--- man/man1/g_traj.1 | 25 ++-- man/man1/g_tune_pme.1 | 60 +++++---- man/man1/g_vanhove.1 | 20 +-- man/man1/g_velacc.1 | 10 +- man/man1/g_wham.1 | 262 ++++++++++++++++++++++--------------- man/man1/g_wheel.1 | 10 +- man/man1/g_x2top.1 | 20 +-- man/man1/g_xrama.1 | 10 +- man/man1/genbox.1 | 41 +++--- man/man1/genconf.1 | 10 +- man/man1/genion.1 | 27 ++-- man/man1/genrestr.1 | 24 ++-- man/man1/gmxcheck.1 | 10 +- man/man1/gmxdump.1 | 8 +- man/man1/grompp.1 | 74 ++++++----- man/man1/make_edi.1 | 102 ++++++++------- man/man1/make_ndx.1 | 10 +- man/man1/mdrun.1 | 99 ++++++++------ man/man1/mk_angndx.1 | 6 +- man/man1/ngmx.1 | 11 +- man/man1/pdb2gmx.1 | 68 +++++----- man/man1/tpbconv.1 | 22 ++-- man/man1/trjcat.1 | 28 ++-- man/man1/trjconv.1 | 67 +++++----- man/man1/trjorder.1 | 12 +- man/man1/xpm2ps.1 | 38 +++--- share/html/online/Makefile.am | 2 +- share/html/online/g_densorder.html | 63 +++++++++ 93 files changed, 1445 insertions(+), 1187 deletions(-) create mode 100644 share/html/online/g_densorder.html diff --git a/admin/programs.txt b/admin/programs.txt index 23d1d94963..affb01d72b 100644 --- a/admin/programs.txt +++ b/admin/programs.txt @@ -139,6 +139,7 @@ HEAD|Interfaces g_potential|calculates the electrostatic potential across the box g_density|calculates the density of the system g_densmap|calculates 2D planar or axial-radial density maps +g_densorder|calculate surface fluctuations g_order|computes the order parameter per atom for carbon tails g_h2order|computes the orientation of water molecules g_bundle|analyzes bundles of axes, e.g. transmembrane helices diff --git a/man/man1/Makefile.am b/man/man1/Makefile.am index 3ad3d4a931..813dd9f898 100644 --- a/man/man1/Makefile.am +++ b/man/man1/Makefile.am @@ -18,6 +18,7 @@ man_MANS = \ g_current.1 \ g_density.1 \ g_densmap.1 \ + g_densorder.1 \ g_dielectric.1 \ g_dih.1 \ g_dipoles.1 \ @@ -32,6 +33,7 @@ man_MANS = \ g_hbond.1 \ g_helix.1 \ g_helixorient.1 \ + g_hydorder.1 \ g_lie.1 \ g_mdmat.1 \ g_membed.1 \ @@ -41,7 +43,9 @@ man_MANS = \ g_nmeig.1 \ g_nmens.1 \ g_nmtraj.1 \ + g_options.1 \ g_order.1 \ + g_pme_error.1 \ g_polystat.1 \ g_potential.1 \ g_principal.1 \ diff --git a/man/man1/do_dssp.1 b/man/man1/do_dssp.1 index 92b9b7afd0..12556d9244 100644 --- a/man/man1/do_dssp.1 +++ b/man/man1/do_dssp.1 @@ -1,8 +1,8 @@ -.TH do_dssp 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME do_dssp - assigns secondary structure and calculates solvent accessible surface area -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3do_dssp\fP .BI "\-f" " traj.xtc " @@ -26,12 +26,13 @@ do_dssp - assigns secondary structure and calculates solvent accessible surface .BI "\-xvg" " enum " .BI "\-sss" " string " .SH DESCRIPTION -\&do_dssp +\&\fB do_dssp\fR \&reads a trajectory file and computes the secondary structure for \&each time frame \&calling the dssp program. If you do not have the dssp program, -\&get it. do_dssp assumes that the dssp executable is -\&/usr/local/bin/dssp. If this is not the case, then you should +\&get it from http://swift.cmbi.ru.nl/gv/dssp. \fB do_dssp\fR assumes +\&that the dssp executable is located in +\&\fB /usr/local/bin/dssp\fR. If this is not the case, then you should \&set an environment variable \fB DSSP\fR pointing to the dssp \&executable, e.g.: @@ -42,7 +43,7 @@ do_dssp - assigns secondary structure and calculates solvent accessible surface \&The structure assignment for each residue and time is written to an \&\fB .xpm\fR matrix file. This file can be visualized with for instance \&\fB xv\fR and can be converted to postscript with \fB xpm2ps\fR. -\&Individual chains are separated by light grey lines in the xpm and +\&Individual chains are separated by light grey lines in the \fB .xpm\fR and \&postscript files. \&The number of residues with each secondary structure type and the \&total secondary structure (\fB \-sss\fR) count as a function of @@ -125,7 +126,7 @@ do_dssp - assigns secondary structure and calculates solvent accessible surface Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/editconf.1 b/man/man1/editconf.1 index 402147ad7b..60126515c4 100644 --- a/man/man1/editconf.1 +++ b/man/man1/editconf.1 @@ -1,8 +1,8 @@ -.TH editconf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME editconf - edits the box and writes subgroups -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3editconf\fP .BI "\-f" " conf.gro " @@ -29,6 +29,7 @@ editconf - edits the box and writes subgroups .BI "\-scale" " vector " .BI "\-density" " real " .BI "\-[no]pbc" "" +.BI "\-resnr" " int " .BI "\-[no]grasp" "" .BI "\-rvdw" " real " .BI "\-sig56" " real " @@ -38,7 +39,7 @@ editconf - edits the box and writes subgroups .BI "\-label" " string " .BI "\-[no]conect" "" .SH DESCRIPTION -\&editconf converts generic structure format to \fB .gro\fR, \fB .g96\fR +\&\fB editconf\fR converts generic structure format to \fB .gro\fR, \fB .g96\fR \&or \fB .pdb\fR. \& @@ -56,18 +57,19 @@ editconf - edits the box and writes subgroups \&The last two are special cases of a triclinic box. \&The length of the three box vectors of the truncated octahedron is the \&shortest distance between two opposite hexagons. -\&The volume of a dodecahedron is 0.71 and that of a truncated octahedron -\&is 0.77 of that of a cubic box with the same periodic image distance. +\&Relative to a cubic box with some periodic image distance, the volume of a +\&dodecahedron with this same periodic distance is 0.71 times that of the cube, +\&and that of a truncated octahedron is 0.77 times. \& \&Option \fB \-box\fR requires only -\&one value for a cubic box, dodecahedron and a truncated octahedron. +\&one value for a cubic, rhombic dodecahedral, or truncated octahedral box. \& -\&With \fB \-d\fR and a \fB triclinic\fR box the size of the system in the x, y -\&and z directions is used. With \fB \-d\fR and \fB cubic\fR, +\&With \fB \-d\fR and a \fB triclinic\fR box the size of the system in the \fI x\fR\-, \fI y\fR\-, +\&and \fI z\fR\-directions is used. With \fB \-d\fR and \fB cubic\fR, \&\fB dodecahedron\fR or \fB octahedron\fR boxes, the dimensions are set \&to the diameter of the system (largest distance between atoms) plus twice \&the specified distance. @@ -75,7 +77,7 @@ editconf - edits the box and writes subgroups \&Option \fB \-angles\fR is only meaningful with option \fB \-box\fR and -\&a triclinic box and can not be used with option \fB \-d\fR. +\&a triclinic box and cannot be used with option \fB \-d\fR. \& @@ -90,17 +92,18 @@ editconf - edits the box and writes subgroups \&\fB \-princ\fR aligns the principal axes of the system along the -\&coordinate axes, this may allow you to decrease the box volume, +\&coordinate axes, with the longest axis aligned with the \fI x\fR\-axis. +\&This may allow you to decrease the box volume, \&but beware that molecules can rotate significantly in a nanosecond. \& \&Scaling is applied before any of the other operations are \&performed. Boxes and coordinates can be scaled to give a certain density (option -\&\fB \-density\fR). Note that this may be inaccurate in case a gro -\&file is given as input. A special feature of the scaling option, when the +\&\fB \-density\fR). Note that this may be inaccurate in case a \fB .gro\fR +\&file is given as input. A special feature of the scaling option is that when the \&factor \-1 is given in one dimension, one obtains a mirror image, -\&mirrored in one of the plains, when one uses \-1 in three dimensions +\&mirrored in one of the planes. When one uses \-1 in three dimensions, \&a point\-mirror image is obtained. @@ -108,7 +111,7 @@ editconf - edits the box and writes subgroups \&Periodicity can be removed in a crude manner. -\&It is important that the box sizes at the bottom of your input file +\&It is important that the box vectors at the bottom of your input file \&are correct when the periodicity is to be removed. \& @@ -126,7 +129,8 @@ editconf - edits the box and writes subgroups \& -\&With the option \-mead a special pdb (pqr) file for the MEAD electrostatics +\&With the option \fB \-mead\fR a special \fB .pdb\fR (\fB .pqr\fR) +\&file for the MEAD electrostatics \&program (Poisson\-Boltzmann solver) can be made. A further prerequisite \&is that the input file is a run input file. \&The B\-factor field is then filled with the Van der Waals radius @@ -134,7 +138,7 @@ editconf - edits the box and writes subgroups \& -\&The option \-grasp is similar, but it puts the charges in the B\-factor +\&The option \fB \-grasp\fR is similar, but it puts the charges in the B\-factor \&and the radius in the occupancy. \& @@ -145,13 +149,13 @@ editconf - edits the box and writes subgroups \& -\&Finally with option \fB \-label\fR editconf can add a chain identifier -\&to a pdb file, which can be useful for analysis with e.g. rasmol. +\&Finally, with option \fB \-label\fR, \fB editconf\fR can add a chain identifier +\&to a \fB .pdb\fR file, which can be useful for analysis with e.g. Rasmol. \& \&To convert a truncated octrahedron file produced by a package which uses -\&a cubic box with the corners cut off (such as Gromos) use: +\&a cubic box with the corners cut off (such as GROMOS), use: \&\fB editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out\fR @@ -188,7 +192,7 @@ editconf - edits the box and writes subgroups Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]ndef" "no " Choose output from default index groups @@ -230,11 +234,14 @@ editconf - edits the box and writes subgroups Scaling factor .BI "\-density" " real" " 1000 " - Density (g/l) of the output box achieved by scaling + Density (g/L) of the output box achieved by scaling .BI "\-[no]pbc" "no " Remove the periodicity (make molecule whole again) +.BI "\-resnr" " int" " \-1" + Renumber residues starting from resnr + .BI "\-[no]grasp" "no " Store the charge of the atom in the B\-factor field and the radius of the atom in the occupancy field @@ -257,12 +264,10 @@ editconf - edits the box and writes subgroups Add chain label for all residues .BI "\-[no]conect" "no " - Add CONECT records to a pdb file when written. Can only be done when a topology is present + Add CONECT records to a \fB .pdb\fR file when written. Can only be done when a topology is present .SH KNOWN PROBLEMS -\- For complex molecules, the periodicity removal routine may break down, - -\- in that case you can use trjconv. +\- For complex molecules, the periodicity removal routine may break down, in that case you can use \fB trjconv\fR. .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/eneconv.1 b/man/man1/eneconv.1 index 6dc846c6e3..631f7213ae 100644 --- a/man/man1/eneconv.1 +++ b/man/man1/eneconv.1 @@ -1,8 +1,8 @@ -.TH eneconv 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME eneconv - converts energy files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3eneconv\fP .BI "\-f" " ener.edr " @@ -16,17 +16,18 @@ eneconv - converts energy files .BI "\-offset" " real " .BI "\-[no]settime" "" .BI "\-[no]sort" "" +.BI "\-[no]rmdh" "" .BI "\-scalefac" " real " .BI "\-[no]error" "" .SH DESCRIPTION \&With \fI multiple files\fR specified for the \fB \-f\fR option: \&Concatenates several energy files in sorted order. -\&In case of double time frames the one +\&In the case of double time frames, the one \&in the later file is used. By specifying \fB \-settime\fR you will be \&asked for the start time of each file. The input files are taken \&from the command line, -\&such that the command \fB eneconv \-o fixed.edr *.edr\fR should do +\&such that the command \fB eneconv \-f *.edr \-o fixed.edr\fR should do \&the trick. @@ -69,7 +70,7 @@ eneconv - converts energy files Only write out frame when t MOD dt = offset .BI "\-offset" " real" " 0 " - Time offset for \-dt option + Time offset for \fB \-dt\fR option .BI "\-[no]settime" "no " Change starting time interactively @@ -77,6 +78,9 @@ eneconv - converts energy files .BI "\-[no]sort" "yes " Sort energy files (not frames) +.BI "\-[no]rmdh" "no " + Remove free energy block data + .BI "\-scalefac" " real" " 1 " Multiply energy component by this factor diff --git a/man/man1/g_anadock.1 b/man/man1/g_anadock.1 index d32edf5f0a..9d14067403 100644 --- a/man/man1/g_anadock.1 +++ b/man/man1/g_anadock.1 @@ -1,8 +1,8 @@ -.TH g_anadock 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_anadock - cluster structures from Autodock runs -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_anadock\fP .BI "\-f" " eiwit.pdb " @@ -18,14 +18,14 @@ g_anadock - cluster structures from Autodock runs .BI "\-[no]rms" "" .BI "\-cutoff" " real " .SH DESCRIPTION -\&anadock analyses the results of an Autodock run and clusters the +\&\fB g_anadock\fR analyses the results of an Autodock run and clusters the \&structures together, based on distance or RMSD. The docked energy \&and free energy estimates are analysed, and for each cluster the \&energy statistics are printed. \&An alternative approach to this is to cluster the structures first -\&(using \fB g_cluster\fR and then sort the clusters on either lowest +\&using \fB g_cluster\fR and then sort the clusters on either lowest \&energy or average energy. .SH FILES .BI "\-f" " eiwit.pdb" diff --git a/man/man1/g_anaeig.1 b/man/man1/g_anaeig.1 index f34e4ed454..febbb0393b 100644 --- a/man/man1/g_anaeig.1 +++ b/man/man1/g_anaeig.1 @@ -1,8 +1,8 @@ -.TH g_anaeig 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_anaeig - analyzes the eigenvectors -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_anaeig\fP .BI "\-v" " eigenvec.trr " @@ -91,12 +91,12 @@ g_anaeig - analyzes the eigenvectors \&\fB \-last\fR have been set explicitly, in which case all eigenvectors \&will be written to separate files. Chain identifiers will be added \&when writing a \fB .pdb\fR file with two or three structures (you -\&can use \fB rasmol \-nmrpdb\fR to view such a pdb file). +\&can use \fB rasmol \-nmrpdb\fR to view such a \fB .pdb\fR file). \& Overlap calculations between covariance analysis: -\& NOTE: the analysis should use the same fitting structure +\& \fB Note:\fR the analysis should use the same fitting structure \&\fB \-over\fR: calculate the subspace overlap of the eigenvectors in @@ -218,7 +218,7 @@ g_anaeig - analyzes the eigenvectors Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_analyze.1 b/man/man1/g_analyze.1 index a9d90fe59e..2ff3a3b248 100644 --- a/man/man1/g_analyze.1 +++ b/man/man1/g_analyze.1 @@ -1,8 +1,8 @@ -.TH g_analyze 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_analyze - analyzes data sets -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_analyze\fP .BI "\-f" " graph.xvg " @@ -47,23 +47,23 @@ g_analyze - analyzes data sets .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_analyze reads an ascii file and analyzes data sets. +\&\fB g_analyze\fR reads an ASCII file and analyzes data sets. \&A line in the input file may start with a time -\&(see option \fB \-time\fR) and any number of y values may follow. +\&(see option \fB \-time\fR) and any number of \fI y\fR\-values may follow. \&Multiple sets can also be -\&read when they are separated by & (option \fB \-n\fR), -\&in this case only one y value is read from each line. +\&read when they are separated by & (option \fB \-n\fR); +\&in this case only one \fI y\fR\-value is read from each line. \&All lines starting with and @ are skipped. \&All analyses can also be done for the derivative of a set \&(option \fB \-d\fR). -\&All options, except for \fB \-av\fR and \fB \-power\fR assume that the +\&All options, except for \fB \-av\fR and \fB \-power\fR, assume that the \&points are equidistant in time. -\&g_analyze always shows the average and standard deviation of each -\&set. For each set it also shows the relative deviation of the third +\&\fB g_analyze\fR always shows the average and standard deviation of each +\&set, as well as the relative deviation of the third \&and fourth cumulant from those of a Gaussian distribution with the same \&standard deviation. @@ -73,7 +73,7 @@ g_analyze - analyzes data sets \&Option \fB \-cc\fR plots the resemblance of set i with a cosine of \&i/2 periods. The formula is: -2 (int0\-T y(t) cos(i pi t) dt)2 / int0\-T y(t) y(t) dt +2 (int0\-T y(t) cos(i [GRK]pi[grk] t) dt)2 / int0\-T y(t) y(t) dt \&This is useful for principal components obtained from covariance \&analysis, since the principal components of random diffusion are @@ -104,13 +104,13 @@ g_analyze - analyzes data sets \&that the autocorrelation is a sum of two exponentials. \&The analytical curve for the block average is: -\&f(t) = sigma sqrt(2/T ( a (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) + +\&f(t) = [GRK]sigma[grk]\fB *\fRsqrt(2/T ( [GRK]alpha[grk] ([GRK]tau[grk]1 ((exp(\-t/[GRK]tau[grk]1) \- 1) [GRK]tau[grk]1/t + 1)) + -\& (1\-a) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))), +\& (1\-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(\-t/[GRK]tau[grk]2) \- 1) [GRK]tau[grk]2/t + 1)))), where T is the total time. -\&a, tau1 and tau2 are obtained by fitting f2(t) to error2. +\&[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f2(t) to error2. \&When the actual block average is very close to the analytical curve, -\&the error is sigma*sqrt(2/T (a tau1 + (1\-a) tau2)). +\&the error is [GRK]sigma[grk]\fB *\fRsqrt(2/T (a [GRK]tau[grk]1 + (1\-a) [GRK]tau[grk]2)). \&The complete derivation is given in \&B. Hess, J. Chem. Phys. 116:209\-217, 2002. @@ -133,7 +133,7 @@ where T is the total time. \&Option \fB \-filter\fR prints the RMS high\-frequency fluctuation \&of each set and over all sets with respect to a filtered average. -\&The filter is proportional to cos(pi t/len) where t goes from \-len/2 +\&The filter is proportional to cos([GRK]pi[grk] t/len) where t goes from \-len/2 \&to len/2. len is supplied with the option \fB \-filter\fR. \&This filter reduces oscillations with period len/2 and len by a factor \&of 0.79 and 0.33 respectively. @@ -145,7 +145,7 @@ where T is the total time. \&Option \fB \-power\fR fits the data to b ta, which is accomplished \&by fitting to a t + b on log\-log scale. All points after the first -\&zero or negative value are ignored. +\&zero or with a negative value are ignored. Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis \&on output from \fB g_hbond\fR. The input file can be taken directly @@ -198,7 +198,7 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -222,7 +222,7 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis Binwidth for the distribution .BI "\-errbar" " enum" " none" - Error bars for \-av: \fB none\fR, \fB stddev\fR, \fB error\fR or \fB 90\fR + Error bars for \fB \-av\fR: \fB none\fR, \fB stddev\fR, \fB error\fR or \fB 90\fR .BI "\-[no]integrate" "no " Integrate data function(s) numerically using trapezium rule @@ -234,10 +234,10 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis Interpret second data set as error in the y values for integrating .BI "\-[no]regression" "no " - Perform a linear regression analysis on the data. If \-xydy is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi2 = (y \- A0 x0 \- A1 x1 \- ... \- AN xN)2 where now Y is the first data set in the input file and xi the others. Do read the information at the option \fB \-time\fR. + Perform a linear regression analysis on the data. If \fB \-xydy\fR is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [GRK]chi[grk]2 = (y \- A0 x0 \- A1 x1 \- ... \- AN xN)2 where now Y is the first data set in the input file and xi the others. Do read the information at the option \fB \-time\fR. .BI "\-[no]luzar" "no " - Do a Luzar and Chandler analysis on a correlation function and related as produced by g_hbond. When in addition the \-xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). + Do a Luzar and Chandler analysis on a correlation function and related as produced by \fB g_hbond\fR. When in addition the \fB \-xydy\fR flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). .BI "\-temp" " real" " 298.15" Temperature for the Luzar hydrogen bonding kinetics analysis @@ -246,10 +246,10 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation .BI "\-fitend" " real" " 60 " - Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with \-gem + Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with \fB \-gem\fR .BI "\-smooth" " real" " \-1 " - If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau) + If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/[GRK]tau[grk]) .BI "\-filter" " real" " 0 " Print the high\-frequency fluctuation after filtering with a cosine filter of length @@ -273,7 +273,7 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_angle.1 b/man/man1/g_angle.1 index f69617ddc5..272c893bd8 100644 --- a/man/man1/g_angle.1 +++ b/man/man1/g_angle.1 @@ -1,8 +1,8 @@ -.TH g_angle 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_angle - calculates distributions and correlations for angles and dihedrals -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_angle\fP .BI "\-f" " traj.xtc " @@ -36,22 +36,22 @@ g_angle - calculates distributions and correlations for angles and dihedrals .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_angle computes the angle distribution for a number of angles +\&\fB g_angle\fR computes the angle distribution for a number of angles \&or dihedrals. This way you can check whether your simulation -\&is correct. With option \-ov you can plot the average angle of -\&a group of angles as a function of time. With the \-all option +\&is correct. With option \fB \-ov\fR you can plot the average angle of +\&a group of angles as a function of time. With the \fB \-all\fR option \&the first graph is the average, the rest are the individual angles. -\&With the \-of option g_angle also calculates the fraction of trans +\&With the \fB \-of\fR option, \fB g_angle\fR also calculates the fraction of trans \&dihedrals (only for dihedrals) as function of time, but this is \&probably only fun for a selected few. -\&With option \-oc a dihedral correlation function is calculated. +\&With option \fB \-oc\fR a dihedral correlation function is calculated. -\&It should be noted that the indexfile should contain +\&It should be noted that the index file should contain \&atom\-triples for angles or atom\-quadruplets for dihedrals. \&If this is not the case, the program will crash. @@ -116,7 +116,7 @@ g_angle - calculates distributions and correlations for angles and dihedrals Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -134,7 +134,7 @@ g_angle - calculates distributions and correlations for angles and dihedrals Print dihedral angles modulo 360 degrees .BI "\-[no]chandler" "no " - Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi \-60 || phi 60. + Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi \-60 or phi 60. .BI "\-[no]avercorr" "no " Average the correlation functions for the individual angles/dihedrals @@ -149,7 +149,7 @@ g_angle - calculates distributions and correlations for angles and dihedrals Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_bar.1 b/man/man1/g_bar.1 index dd4a4f440e..824d5af1b6 100644 --- a/man/man1/g_bar.1 +++ b/man/man1/g_bar.1 @@ -1,15 +1,15 @@ -.TH g_bar 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_bar - calculates free energy difference estimates through Bennett's acceptance ratio -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_bar\fP .BI "\-f" " dhdl.xvg " +.BI "\-g" " ener.edr " .BI "\-o" " bar.xvg " .BI "\-oi" " barint.xvg " .BI "\-oh" " histogram.xvg " -.BI "\-g" " energy.edr " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " @@ -23,42 +23,73 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance .BI "\-nbmax" " int " .BI "\-nbin" " int " .SH DESCRIPTION -\&g_bar calculates free energy difference estimates through -\&Bennett's acceptance ratio method. -\&Input option \fB \-f\fR expects multiple dhdl files. +\&\fB g_bar\fR calculates free energy difference estimates through +\&Bennett's acceptance ratio method (BAR). It also automatically +\&adds series of individual free energies obtained with BAR into +\&a combined free energy estimate. + + +\&Every individual BAR free energy difference relies on two +\&simulations at different states: say state A and state B, as +\&controlled by a parameter, [GRK]lambda[grk] (see the \fB .mdp\fR parameter +\&\fB init_lambda\fR). The BAR method calculates a ratio of weighted +\&average of the Hamiltonian difference of state B given state A and +\&vice versa. If the Hamiltonian does not depend linearly on [GRK]lambda[grk] +\&(in which case we can extrapolate the derivative of the Hamiltonian +\&with respect to [GRK]lambda[grk], as is the default when \fB free_energy\fR is on), +\&the energy differences to the other state need to be calculated +\&explicitly during the simulation. This can be controlled with +\&the \fB .mdp\fR option \fB foreign_lambda\fR. + + +\&Input option \fB \-f\fR expects multiple \fB dhdl.xvg\fR files. \&Two types of input files are supported: -\&* Files with only one y\-value, for such files it is assumed -\&that the y\-value is dH/dlambda and that the Hamiltonian depends -\&linearly on lambda. The lambda value of the simulation is inferred -\&from the subtitle if present, otherwise from a number in the -\&subdirectory in the file name. +\&\fB *\fR Files with only one \fI y\fR\-value, for such files it is assumed +\& that the \fI y\fR\-value is dH/d[GRK]lambda[grk] and that the Hamiltonian depends +\& linearly on [GRK]lambda[grk]. The [GRK]lambda[grk] value of the simulation is inferred +\& from the subtitle (if present), otherwise from a number in the +\& subdirectory in the file name. \& -\&* Files with more than one y\-value. The files should have columns -\&with dH/dlambda and Delta lambda. The lambda values are inferred -\&from the legends: -\&lambda of the simulation from the legend of dH/dlambda -\&and the foreign lambda's from the legends of Delta H. +\&\fB *\fR Files with more than one \fI y\fR\-value. The files should have columns +\& with dH/d[GRK]lambda[grk] and [GRK]Delta[grk][GRK]lambda[grk]. The [GRK]lambda[grk] values are inferred +\& from the legends: [GRK]lambda[grk] of the simulation from the legend of dH/d[GRK]lambda[grk] +\& and the foreign [GRK]lambda[grk] values from the legends of Delta H. -\&The lambda of the simulation is parsed from dhdl.xvg file's legend -\&containing the string 'dH', the foreign lambda's from the legend +\&The [GRK]lambda[grk] of the simulation is parsed from \fB dhdl.xvg\fR file's legend +\&containing the string 'dH', the foreign [GRK]lambda[grk] values from the legend \&containing the capitalized letters 'D' and 'H'. The temperature \&is parsed from the legend line containing 'T ='. -\&The free energy estimates are determined using BAR with bisection, -\&the precision of the output is set with \fB \-prec\fR. +\&The input option \fB \-g\fR expects multiple \fB .edr\fR files. +\&These can contain either lists of energy differences (see the +\&\fB .mdp\fR option \fB separate_dhdl_file\fR), or a series of histograms +\&(see the \fB .mdp\fR options \fB dh_hist_size\fR and \fB dh_hist_spacing\fR). +\&The temperature and [GRK]lambda[grk] values are automatically deduced from +\&the \fB ener.edr\fR file. + +The free energy estimates are determined using BAR with bisection, +\&with the precision of the output set with \fB \-prec\fR. \&An error estimate taking into account time correlations \&is made by splitting the data into blocks and determining \&the free energy differences over those blocks and assuming \&the blocks are independent. \&The final error estimate is determined from the average variance -\&over 5 blocks. A range of blocks numbers for error estimation can +\&over 5 blocks. A range of block numbers for error estimation can \&be provided with the options \fB \-nbmin\fR and \fB \-nbmax\fR. +\&\fB g_bar\fR tries to aggregate samples with the same 'native' and 'foreign' +\&[GRK]lambda[grk] values, but always assumes independent samples. \fB Note\fR that +\&when aggregating energy differences/derivatives with different +\&sampling intervals, this is almost certainly not correct. Usually +\&subsequent energies are correlated and different time intervals mean +\&different degrees of correlation between samples. + + \&The results are split in two parts: the last part contains the final \&results in kJ/mol, together with the error estimate for each part \&and the total. The first part contains detailed free energy @@ -66,17 +97,17 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance \&kT (together with their computed error estimate). The printed \&values are: -\&* lam_A: the lambda values for point A. +\&\fB *\fR lam_A: the [GRK]lambda[grk] values for point A. -\&* lam_B: the lambda values for point B. +\&\fB *\fR lam_B: the [GRK]lambda[grk] values for point B. -\&* DG: the free energy estimate. +\&\fB *\fR DG: the free energy estimate. -\&* s_A: an estimate of the relative entropy of B in A. +\&\fB *\fR s_A: an estimate of the relative entropy of B in A. -\&* s_A: an estimate of the relative entropy of A in B. +\&\fB *\fR s_A: an estimate of the relative entropy of A in B. -\&* stdev: an estimate expected per\-sample standard deviation. +\&\fB *\fR stdev: an estimate expected per\-sample standard deviation. \&The relative entropy of both states in each other's ensemble can be @@ -85,15 +116,19 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance \&ensemble of lambda_A (and vice versa for s_B), is a \&measure of the 'distance' between Boltzmann distributions of \&the two states, that goes to zero for identical distributions. See -\&Wu & Kofke, J. Chem. Phys. 123 084109 (2009) for more information. +\&Wu & Kofke, J. Chem. Phys. 123 084109 (2005) for more information. \& \&The estimate of the expected per\-sample standard deviation, as given -\&in Bennett's original BAR paper: -\&Bennett, J. Comp. Phys. 22, p 245 (1976), Eq. 10 gives an estimate -\&of the quality of sampling (not directly of the actual statistical -\&error, because it assumes independent samples). +\&in Bennett's original BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976). +\&Eq. 10 therein gives an estimate of the quality of sampling (not directly +\&of the actual statistical error, because it assumes independent samples). + + +\&To get a visual estimate of the phase space overlap, use the +\&\fB \-oh\fR option to write series of histograms, together with the +\&\fB \-nbin\fR option. .SH FILES @@ -101,6 +136,10 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance .B Input, Opt., Mult. xvgr/xmgr file +.BI "\-g" " ener.edr" +.B Input, Opt., Mult. + Energy file + .BI "\-o" " bar.xvg" .B Output, Opt. xvgr/xmgr file @@ -113,10 +152,6 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance .B Output, Opt. xvgr/xmgr file -.BI "\-g" " energy.edr" -.B Input, Opt., Mult. - Energy file - .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit @@ -128,7 +163,7 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_bond.1 b/man/man1/g_bond.1 index ec92658e2e..44c354d488 100644 --- a/man/man1/g_bond.1 +++ b/man/man1/g_bond.1 @@ -1,8 +1,8 @@ -.TH g_bond 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_bond - calculates distances between atoms -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_bond\fP .BI "\-f" " traj.xtc " @@ -24,8 +24,8 @@ g_bond - calculates distances between atoms .BI "\-[no]aver" "" .BI "\-[no]averdist" "" .SH DESCRIPTION -\&g_bond makes a distribution of bond lengths. If all is well a -\&gaussian distribution should be made when using a harmonic potential. +\&\fB g_bond\fR makes a distribution of bond lengths. If all is well a +\&Gaussian distribution should be made when using a harmonic potential. \&Bonds are read from a single group in the index file in order i1\-j1 \&i2\-j2 through in\-jn. @@ -84,7 +84,7 @@ g_bond - calculates distances between atoms Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -99,7 +99,7 @@ g_bond - calculates distances between atoms Average bond length distributions .BI "\-[no]averdist" "yes " - Average distances (turns on \-d) + Average distances (turns on \fB \-d\fR) .SH KNOWN PROBLEMS \- It should be possible to get bond information from the topology. diff --git a/man/man1/g_bundle.1 b/man/man1/g_bundle.1 index ad8275809d..72b0f6a23e 100644 --- a/man/man1/g_bundle.1 +++ b/man/man1/g_bundle.1 @@ -1,8 +1,8 @@ -.TH g_bundle 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_bundle - analyzes bundles of axes, e.g. helices -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_bundle\fP .BI "\-f" " traj.xtc " @@ -29,7 +29,7 @@ g_bundle - analyzes bundles of axes, e.g. helices .BI "\-na" " int " .BI "\-[no]z" "" .SH DESCRIPTION -\&g_bundle analyzes bundles of axes. The axes can be for instance +\&\fB g_bundle\fR analyzes bundles of axes. The axes can be for instance \&helix axes. The program reads two index groups and divides both \&of them in \fB \-na\fR parts. The centers of mass of these parts \&define the tops and bottoms of the axes. @@ -50,8 +50,8 @@ g_bundle - analyzes bundles of axes, e.g. helices \&With option \fB \-oa\fR the top, mid (or kink when \fB \-ok\fR is set) \&and bottom points of each axis -\&are written to a pdb file each frame. The residue numbers correspond -\&to the axis numbers. When viewing this file with \fB rasmol\fR, use the +\&are written to a \fB .pdb\fR file each frame. The residue numbers correspond +\&to the axis numbers. When viewing this file with Rasmol, use the \&command line option \fB \-nmrpdb\fR, and type \fB set axis true\fR to \&display the reference axis. .SH FILES @@ -136,7 +136,7 @@ g_bundle - analyzes bundles of axes, e.g. helices Number of axes .BI "\-[no]z" "no " - Use the Z\-axis as reference iso the average axis + Use the \fI z\fR\-axis as reference instead of the average axis .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_chi.1 b/man/man1/g_chi.1 index d43c71c62e..c4d6b17232 100644 --- a/man/man1/g_chi.1 +++ b/man/man1/g_chi.1 @@ -1,8 +1,8 @@ -.TH g_chi 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_chi - calculates everything you want to know about chi and other dihedrals -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_chi\fP .BI "\-s" " conf.gro " @@ -52,25 +52,25 @@ g_chi - calculates everything you want to know about chi and other dihedrals .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_chi computes phi, psi, omega and chi dihedrals for all your +\&\fB g_chi\fR computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your \&amino acid backbone and sidechains. \&It can compute dihedral angle as a function of time, and as \&histogram distributions. -\&The distributions (histo\-(dihedral)(RESIDUE).xvg) are cumulative over all residues of each type. +\&The distributions \fB (histo\-(dihedral)(RESIDUE).xvg\fR) are cumulative over all residues of each type. \&If option \fB \-corr\fR is given, the program will \&calculate dihedral autocorrelation functions. The function used -\&is C(t) = cos(chi(tau)) cos(chi(tau+t)) . The use of cosines +\&is C(t) = cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) . The use of cosines \&rather than angles themselves, resolves the problem of periodicity. -\&(Van der Spoel & Berendsen (1997), \fB Biophys. J. 72\fR, 2032\-2041). +\&(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032\-2041). \&Separate files for each dihedral of each residue -\&(corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a +\&\fB (corr(dihedral)(RESIDUE)(nresnr).xvg\fR) are output, as well as a \&file containing the information for all residues (argument of \fB \-corr\fR). \&With option \fB \-all\fR, the angles themselves as a function of time for -\&each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg. +\&each residue are printed to separate files \fB (dihedral)(RESIDUE)(nresnr).xvg\fR. \&These can be in radians or degrees. @@ -85,37 +85,38 @@ g_chi - calculates everything you want to know about chi and other dihedrals \&(d) a table for each residue of the rotamer occupancy. -\&All rotamers are taken as 3\-fold, except for omegas and chi\-dihedrals -\&to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu -\&and gln, and chi4 of arg), which are 2\-fold. "rotamer 0" means + +\&All rotamers are taken as 3\-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals +\&to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu +\&and Gln; and [GRK]chi[grk]4 of Arg), which are 2\-fold. "rotamer 0" means \&that the dihedral was not in the core region of each rotamer. \&The width of the core region can be set with \fB \-core_rotamer\fR -\&The S2 order parameters are also output to an xvg file -\&(argument \fB \-o\fR ) and optionally as a pdb file with +\&The S2 order parameters are also output to an \fB .xvg\fR file +\&(argument \fB \-o\fR ) and optionally as a \fB .pdb\fR file with \&the S2 values as B\-factor (argument \fB \-p\fR). \&The total number of rotamer transitions per timestep \&(argument \fB \-ot\fR), the number of transitions per rotamer \&(argument \fB \-rt\fR), and the 3J couplings (argument \fB \-jc\fR), -\&can also be written to .xvg files. +\&can also be written to \fB .xvg\fR files. -\&If \fB \-chi_prod\fR is set (and maxchi 0), cumulative rotamers, e.g. -\&1+9(chi1\-1)+3(chi2\-1)+(chi3\-1) (if the residue has three 3\-fold -\&dihedrals and maxchi = 3) +\&If \fB \-chi_prod\fR is set (and \fB \-maxchi\fR 0), cumulative rotamers, e.g. +\&1+9([GRK]chi[grk]1\-1)+3([GRK]chi[grk]2\-1)+([GRK]chi[grk]3\-1) (if the residue has three 3\-fold +\&dihedrals and \fB \-maxchi\fR = 3) \&are calculated. As before, if any dihedral is not in the core region, \&the rotamer is taken to be 0. The occupancies of these cumulative \&rotamers (starting with rotamer 0) are written to the file \&that is the argument of \fB \-cp\fR, and if the \fB \-all\fR flag \&is given, the rotamers as functions of time -\&are written to chiproduct(RESIDUE)(nresnr).xvg -\&and their occupancies to histo\-chiproduct(RESIDUE)(nresnr).xvg. +\&are written to \fB chiproduct(RESIDUE)(nresnr).xvg\fR +\&and their occupancies to \fB histo\-chiproduct(RESIDUE)(nresnr).xvg\fR. -\&The option \fB \-r\fR generates a contour plot of the average omega angle -\&as a function of the phi and psi angles, that is, in a Ramachandran plot -\&the average omega angle is plotted using color coding. +\&The option \fB \-r\fR generates a contour plot of the average [GRK]omega[grk] angle +\&as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot +\&the average [GRK]omega[grk] angle is plotted using color coding. .SH FILES .BI "\-s" " conf.gro" .B Input @@ -185,7 +186,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -194,16 +195,16 @@ g_chi - calculates everything you want to know about chi and other dihedrals starting residue .BI "\-[no]phi" "no " - Output for Phi dihedral angles + Output for [GRK]phi[grk] dihedral angles .BI "\-[no]psi" "no " - Output for Psi dihedral angles + Output for [GRK]psi[grk] dihedral angles .BI "\-[no]omega" "no " - Output for Omega dihedrals (peptide bonds) + Output for [GRK]omega[grk] dihedrals (peptide bonds) .BI "\-[no]rama" "no " - Generate Phi/Psi and Chi1/Chi2 ramachandran plots + Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots .BI "\-[no]viol" "no " Write a file that gives 0 or 1 for violated Ramachandran angles @@ -218,25 +219,25 @@ g_chi - calculates everything you want to know about chi and other dihedrals in angle vs time files, use radians rather than degrees. .BI "\-[no]shift" "no " - Compute chemical shifts from Phi/Psi angles + Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles .BI "\-binwidth" " int" " 1" bin width for histograms (degrees) .BI "\-core_rotamer" " real" " 0.5 " - only the central \-core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) + only the central \fB \-core_rotamer\fR*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) .BI "\-maxchi" " enum" " 0" - calculate first ndih Chi dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR + calculate first ndih [GRK]chi[grk] dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR .BI "\-[no]normhisto" "yes " Normalize histograms .BI "\-[no]ramomega" "no " - compute average omega as a function of phi/psi and plot it in an xpm plot + compute average omega as a function of phi/psi and plot it in an \fB .xpm\fR plot .BI "\-bfact" " real" " \-1 " - B\-factor value for pdb file for atoms with no calculated dihedral order parameter + B\-factor value for \fB .pdb\fR file for atoms with no calculated dihedral order parameter .BI "\-[no]chi_prod" "no " compute a single cumulative rotamer for each residue @@ -245,7 +246,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals Include dihedrals to sidechain hydrogens .BI "\-bmax" " real" " 0 " - Maximum B\-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X\-Ray structures is analyzed. \-bmax = 0 means no limit. + Maximum B\-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X\-Ray structures is analyzed. \fB \-bmax\fR = 0 means no limit. .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames @@ -257,7 +258,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions @@ -271,11 +272,11 @@ g_chi - calculates everything you want to know about chi and other dihedrals .SH KNOWN PROBLEMS \- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output. -\- Phi and psi dihedrals are calculated in a non\-standard way, using H\-N\-CA\-C for phi instead of C(\-)\-N\-CA\-C, and N\-CA\-C\-O for psi instead of N\-CA\-C\-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama. +\- [GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non\-standard way, using H\-N\-CA\-C for [GRK]phi[grk] instead of C(\-)\-N\-CA\-C, and N\-CA\-C\-O for [GRK]psi[grk] instead of N\-CA\-C\-N(+). This causes (usually small) discrepancies with the output of other tools like \fB g_rama\fR. -\- \-r0 option does not work properly +\- \fB \-r0\fR option does not work properly -\- Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0 +\- Rotamers with multiplicity 2 are printed in \fB chi.log\fR as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0 .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_cluster.1 b/man/man1/g_cluster.1 index d18de12d3d..cda3f76ba5 100644 --- a/man/man1/g_cluster.1 +++ b/man/man1/g_cluster.1 @@ -1,8 +1,8 @@ -.TH g_cluster 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_cluster - clusters structures -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_cluster\fP .BI "\-f" " traj.xtc " @@ -45,10 +45,11 @@ g_cluster - clusters structures .BI "\-seed" " int " .BI "\-niter" " int " .BI "\-kT" " real " +.BI "\-[no]pbc" "" .SH DESCRIPTION -\&g_cluster can cluster structures with several different methods. +\&\fB g_cluster\fR can cluster structures using several different methods. \&Distances between structures can be determined from a trajectory -\&or read from an XPM matrix file with the \fB \-dm\fR option. +\&or read from an \fB .xpm\fR matrix file with the \fB \-dm\fR option. \&RMS deviation after fitting or RMS deviation of atom\-pair distances \&can be used to define the distance between structures. @@ -74,7 +75,7 @@ g_cluster - clusters structures \&(\fI Angew. Chem. Int. Ed.\fR \fB 1999\fR, \fI 38\fR, pp 236\-240). \&Count number of neighbors using cut\-off, take structure with \&largest number of neighbors with all its neighbors as cluster -\&and eleminate it from the pool of clusters. Repeat for remaining +\&and eliminate it from the pool of clusters. Repeat for remaining \&structures in pool. @@ -198,7 +199,7 @@ g_cluster - clusters structures Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -237,10 +238,10 @@ g_cluster - clusters structures Method for cluster determination: \fB linkage\fR, \fB jarvis\-patrick\fR, \fB monte\-carlo\fR, \fB diagonalization\fR or \fB gromos\fR .BI "\-minstruct" " int" " 1" - Minimum number of structures in cluster for coloring in the xpm file + Minimum number of structures in cluster for coloring in the \fB .xpm\fR file .BI "\-[no]binary" "no " - Treat the RMSD matrix as consisting of 0 and 1, where the cut\-off is given by \-cutoff + Treat the RMSD matrix as consisting of 0 and 1, where the cut\-off is given by \fB \-cutoff\fR .BI "\-M" " int" " 10" Number of nearest neighbors considered for Jarvis\-Patrick algorithm, 0 is use cutoff @@ -257,6 +258,9 @@ g_cluster - clusters structures .BI "\-kT" " real" " 0.001 " Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) +.BI "\-[no]pbc" "yes " + PBC check + .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_clustsize.1 b/man/man1/g_clustsize.1 index 07e2885874..a78bcc07a8 100644 --- a/man/man1/g_clustsize.1 +++ b/man/man1/g_clustsize.1 @@ -1,8 +1,8 @@ -.TH g_clustsize 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_clustsize - calculate size distributions of atomic clusters -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_clustsize\fP .BI "\-f" " traj.xtc " @@ -35,8 +35,8 @@ g_clustsize - calculate size distributions of atomic clusters .BI "\-rgbhi" " vector " .SH DESCRIPTION \&This program computes the size distributions of molecular/atomic clusters in -\&the gas phase. The output is given in the form of a XPM file. -\&The total number of clusters is written to a XVG file. +\&the gas phase. The output is given in the form of an \fB .xpm\fR file. +\&The total number of clusters is written to an \fB .xvg\fR file. \&When the \fB \-mol\fR option is given clusters will be made out of @@ -46,11 +46,11 @@ g_clustsize - calculate size distributions of atomic clusters \&When velocities are present in your trajectory, the temperature of -\&the largest cluster will be printed in a separate xvg file assuming +\&the largest cluster will be printed in a separate \fB .xvg\fR file assuming \&that the particles are free to move. If you are using constraints, \&please correct the temperature. For instance water simulated with SHAKE \&or SETTLE will yield a temperature that is 1.5 times too low. You can -\&compensate for this with the \-ndf option. Remember to take the removal +\&compensate for this with the \fB \-ndf\fR option. Remember to take the removal \&of center of mass motion into account. @@ -124,7 +124,7 @@ g_clustsize - calculate size distributions of atomic clusters Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -133,7 +133,7 @@ g_clustsize - calculate size distributions of atomic clusters Largest distance (nm) to be considered in a cluster .BI "\-[no]mol" "no " - Cluster molecules rather than atoms (needs tpr file) + Cluster molecules rather than atoms (needs \fB .tpr\fR file) .BI "\-[no]pbc" "yes " Use periodic boundary conditions @@ -142,7 +142,7 @@ g_clustsize - calculate size distributions of atomic clusters Number of frames to skip between writing .BI "\-nlevels" " int" " 20" - Number of levels of grey in xpm output + Number of levels of grey in \fB .xpm\fR output .BI "\-ndf" " int" " \-1" Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used. diff --git a/man/man1/g_confrms.1 b/man/man1/g_confrms.1 index 4c31798dbf..6f99dffb23 100644 --- a/man/man1/g_confrms.1 +++ b/man/man1/g_confrms.1 @@ -1,8 +1,8 @@ -.TH g_confrms 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_confrms - fits two structures and calculates the rmsd -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_confrms\fP .BI "\-f1" " conf1.gro " @@ -23,8 +23,8 @@ g_confrms - fits two structures and calculates the rmsd .BI "\-[no]label" "" .BI "\-[no]bfac" "" .SH DESCRIPTION -\&g_confrms computes the root mean square deviation (RMSD) of two -\&structures after LSQ fitting the second structure on the first one. +\&\fB g_confrms\fR computes the root mean square deviation (RMSD) of two +\&structures after least\-squares fitting the second structure on the first one. \&The two structures do NOT need to have the same number of atoms, \&only the two index groups used for the fit need to be identical. \&With \fB \-name\fR only matching atom names from the selected groups @@ -73,7 +73,7 @@ g_confrms - fits two structures and calculates the rmsd Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]one" "no " Only write the fitted structure to file diff --git a/man/man1/g_covar.1 b/man/man1/g_covar.1 index 39cedbc3c6..9793b8157b 100644 --- a/man/man1/g_covar.1 +++ b/man/man1/g_covar.1 @@ -1,8 +1,8 @@ -.TH g_covar 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_covar - calculates and diagonalizes the covariance matrix -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_covar\fP .BI "\-f" " traj.xtc " @@ -56,13 +56,22 @@ g_covar - calculates and diagonalizes the covariance matrix \& -\&Option \fB \-xpm\fR writes the whole covariance matrix to an xpm file. +\&Option \fB \-xpm\fR writes the whole covariance matrix to an \fB .xpm\fR file. \& -\&Option \fB \-xpma\fR writes the atomic covariance matrix to an xpm file, +\&Option \fB \-xpma\fR writes the atomic covariance matrix to an \fB .xpm\fR file, \&i.e. for each atom pair the sum of the xx, yy and zz covariances is \&written. +\& + + +\&Note that the diagonalization of a matrix requires memory and time +\&that will increase at least as fast as than the square of the number +\&of atoms involved. It is easy to run out of memory, in which +\&case this tool will probably exit with a 'Segmentation fault'. You +\&should consider carefully whether a reduced set of atoms will meet +\&your needs for lower costs. .SH FILES .BI "\-f" " traj.xtc" .B Input diff --git a/man/man1/g_current.1 b/man/man1/g_current.1 index 8a02558c22..dda3b71a12 100644 --- a/man/man1/g_current.1 +++ b/man/man1/g_current.1 @@ -1,8 +1,8 @@ -.TH g_current 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_current - calculate current autocorrelation function of system -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_current\fP .BI "\-s" " topol.tpr " @@ -32,17 +32,17 @@ g_current - calculate current autocorrelation function of system .BI "\-tr" " real " .BI "\-temp" " real " .SH DESCRIPTION -\&This is a tool for calculating the current autocorrelation function, the correlation +\&\fB g_current\fR is a tool for calculating the current autocorrelation function, the correlation \&of the rotational and translational dipole moment of the system, and the resulting static -\&dielectric constant. To obtain a reasonable result the index group has to be neutral. -\&Furthermore the routine is capable of extracting the static conductivity from the current -\&autocorrelation function, if velocities are given. Additionally an Einstein\-Helfand fit also -\&allows to get the static conductivity. +\&dielectric constant. To obtain a reasonable result, the index group has to be neutral. +\&Furthermore, the routine is capable of extracting the static conductivity from the current +\&autocorrelation function, if velocities are given. Additionally, an Einstein\-Helfand fit +\&can be used to obtain the static conductivity. \&The flag \fB \-caf\fR is for the output of the current autocorrelation function and \fB \-mc\fR writes the \&correlation of the rotational and translational part of the dipole moment in the corresponding -\&file. However this option is only available for trajectories containing velocities. +\&file. However, this option is only available for trajectories containing velocities. \&Options \fB \-sh\fR and \fB \-tr\fR are responsible for the averaging and integration of the \&autocorrelation functions. Since averaging proceeds by shifting the starting point \&through the trajectory, the shift can be modified with \fB \-sh\fR to enable the choice of uncorrelated @@ -64,10 +64,10 @@ g_current - calculate current autocorrelation function of system \&\fB \-[no]nojump\fR unfolds the coordinates to allow free diffusion. This is required to get a continuous -\&translational dipole moment, required for the Einstein\-Helfand fit. The resuls from the fit allow to -\&determine the dielectric constant for system of charged molecules. However it is also possible to extract +\&translational dipole moment, required for the Einstein\-Helfand fit. The results from the fit allow +\&the determination of the dielectric constant for system of charged molecules. However, it is also possible to extract \&the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this -\&options has to be used with care, since only very short time spans fulfill the approximation, that the density +\&option has to be used with care, since only very short time spans fulfill the approximation that the density \&of the molecules is approximately constant and the averages are already converged. To be on the safe side, \&the dielectric constant should be calculated with the help of the Einstein\-Helfand method for \&the translational part of the dielectric constant. @@ -128,7 +128,7 @@ g_current - calculate current autocorrelation function of system Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -140,7 +140,7 @@ g_current - calculate current autocorrelation function of system Removes jumps of atoms across the box. .BI "\-eps" " real" " 0 " - Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (thinfoil boundary conditions). + Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (tin\-foil boundary conditions). .BI "\-bfit" " real" " 100 " Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment. diff --git a/man/man1/g_density.1 b/man/man1/g_density.1 index e4334a3cdf..e86623db52 100644 --- a/man/man1/g_density.1 +++ b/man/man1/g_density.1 @@ -1,8 +1,8 @@ -.TH g_density 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_density - calculates the density of the system -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_density\fP .BI "\-f" " traj.xtc " @@ -25,17 +25,23 @@ g_density - calculates the density of the system .BI "\-[no]symm" "" .BI "\-[no]center" "" .SH DESCRIPTION -\&Compute partial densities across the box, using an index file. Densities -\&in kg/m3, number densities or electron densities can be +\&Compute partial densities across the box, using an index file. + + +\&For the total density of NPT simulations, use \fB g_energy\fR instead. +\& + + +\&Densities are in kg/m3, and number densities or electron densities can also be \&calculated. For electron densities, a file describing the number of \&electrons for each type of atom should be provided using \fB \-ei\fR. \&It should look like: -\& 2 +\& \fB 2\fR -\& atomname = nrelectrons +\& \fB atomname = nrelectrons\fR -\& atomname = nrelectrons +\& \fB atomname = nrelectrons\fR \&The first line contains the number of lines to read from the file. \&There should be one line for each unique atom name in your system. @@ -82,7 +88,7 @@ g_density - calculates the density of the system Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_densmap.1 b/man/man1/g_densmap.1 index 7683711286..96b59fe837 100644 --- a/man/man1/g_densmap.1 +++ b/man/man1/g_densmap.1 @@ -1,8 +1,8 @@ -.TH g_densmap 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_densmap - calculates 2D planar or axial-radial density maps -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_densmap\fP .BI "\-f" " traj.xtc " @@ -31,11 +31,11 @@ g_densmap - calculates 2D planar or axial-radial density maps .BI "\-dmin" " real " .BI "\-dmax" " real " .SH DESCRIPTION -\&g_densmap computes 2D number\-density maps. +\&\fB g_densmap\fR computes 2D number\-density maps. \&It can make planar and axial\-radial density maps. \&The output \fB .xpm\fR file can be visualized with for instance xv -\&and can be converted to postscript with xpm2ps. -\&Optionally, output can be in text form to a .dat file. +\&and can be converted to postscript with \fB xpm2ps\fR. +\&Optionally, output can be in text form to a \fB .dat\fR file with \fB \-od\fR, instead of the usual \fB .xpm\fR file with \fB \-o\fR. \& @@ -110,7 +110,7 @@ g_densmap - calculates 2D planar or axial-radial density maps Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-bin" " real" " 0.02 " Grid size (nm) diff --git a/man/man1/g_dielectric.1 b/man/man1/g_dielectric.1 index a10fee14a0..a3f24fd193 100644 --- a/man/man1/g_dielectric.1 +++ b/man/man1/g_dielectric.1 @@ -1,8 +1,8 @@ -.TH g_dielectric 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_dielectric - calculates frequency dependent dielectric constants -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_dielectric\fP .BI "\-f" " dipcorr.xvg " @@ -32,19 +32,22 @@ g_dielectric - calculates frequency dependent dielectric constants .BI "\-ffn" " enum " .BI "\-nsmooth" " int " .SH DESCRIPTION -\&dielectric calculates frequency dependent dielectric constants +\&\fB g_dielectric\fR calculates frequency dependent dielectric constants \&from the autocorrelation function of the total dipole moment in -\&your simulation. This ACF can be generated by g_dipoles. +\&your simulation. This ACF can be generated by \fB g_dipoles\fR. \&For an estimate of the error you can run g_statistics on the \&ACF, and use the output thus generated for this program. \&The functional forms of the available functions are: -\&One parameter : y = Exp[\-a1 x], -\&Two parameters : y = a2 Exp[\-a1 x], +\&One parameter: y = Exp[\-a1 x], + +\&Two parameters: y = a2 Exp[\-a1 x], + \&Three parameters: y = a2 Exp[\-a1 x] + (1 \- a2) Exp[\-a3 x]. + \&Start values for the fit procedure can be given on the command line. -\&It is also possible to fix parameters at their start value, use \-fix +\&It is also possible to fix parameters at their start value, use \fB \-fix\fR \&with the number of the parameter you want to fix. \& @@ -95,7 +98,7 @@ g_dielectric - calculates frequency dependent dielectric constants Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -104,10 +107,10 @@ g_dielectric - calculates frequency dependent dielectric constants use fast fourier transform for correlation function .BI "\-[no]x1" "yes " - use first column as X axis rather than first data set + use first column as \fI x\fR\-axis rather than first data set .BI "\-eint" " real" " 5 " - Time were to end the integration of the data and start to use the fit + Time to end the integration of the data and start to use the fit .BI "\-bfit" " real" " 5 " Begin time of fit @@ -122,22 +125,22 @@ g_dielectric - calculates frequency dependent dielectric constants Start value for fit parameter A .BI "\-tau1" " real" " 10 " - Start value for fit parameter tau1 + Start value for fit parameter [GRK]tau[grk]1 .BI "\-tau2" " real" " 1 " - Start value for fit parameter tau2 + Start value for fit parameter [GRK]tau[grk]2 .BI "\-eps0" " real" " 80 " - Epsilon 0 of your liquid + [GRK]epsilon[grk]0 of your liquid .BI "\-epsRF" " real" " 78.5 " - Epsilon of the reaction field used in your simulation. A value of 0 means infinity. + [GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity. .BI "\-fix" " int" " 0" Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) .BI "\-ffn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-nsmooth" " int" " 3" Number of points for smoothing diff --git a/man/man1/g_dih.1 b/man/man1/g_dih.1 index aa6624a081..76bd72b8c1 100644 --- a/man/man1/g_dih.1 +++ b/man/man1/g_dih.1 @@ -1,8 +1,8 @@ -.TH g_dih 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_dih - analyzes dihedral transitions -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_dih\fP .BI "\-f" " traj.xtc " @@ -18,7 +18,7 @@ g_dih - analyzes dihedral transitions .BI "\-[no]sa" "" .BI "\-mult" " int " .SH DESCRIPTION -\&g_dih can do two things. The default is to analyze dihedral transitions +\&\fB g_dih\fR can do two things. The default is to analyze dihedral transitions \&by merely computing all the dihedral angles defined in your topology \&for the whole trajectory. When a dihedral flips over to another minimum \&an angle/time plot is made. @@ -61,7 +61,7 @@ g_dih - analyzes dihedral transitions Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]sa" "no " Perform cluster analysis in dihedral space instead of analysing dihedral transitions. diff --git a/man/man1/g_dipoles.1 b/man/man1/g_dipoles.1 index ea960c9a43..a3b6ae7927 100644 --- a/man/man1/g_dipoles.1 +++ b/man/man1/g_dipoles.1 @@ -1,8 +1,8 @@ -.TH g_dipoles 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_dipoles - computes the total dipole plus fluctuations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_dipoles\fP .BI "\-en" " ener.edr " @@ -53,24 +53,24 @@ g_dipoles - computes the total dipole plus fluctuations .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_dipoles computes the total dipole plus fluctuations of a simulation +\&\fB g_dipoles\fR computes the total dipole plus fluctuations of a simulation \&system. From this you can compute e.g. the dielectric constant for -\&low dielectric media. +\&low\-dielectric media. \&For molecules with a net charge, the net charge is subtracted at \¢er of mass of the molecule. -\&The file Mtot.xvg contains the total dipole moment of a frame, the +\&The file \fB Mtot.xvg\fR contains the total dipole moment of a frame, the \&components as well as the norm of the vector. -\&The file aver.xvg contains |Mu|2 and | Mu |2 during the +\&The file \fB aver.xvg\fR contains |Mu|2 and | Mu |2 during the \&simulation. -\&The file dipdist.xvg contains the distribution of dipole moments during +\&The file \fB dipdist.xvg\fR contains the distribution of dipole moments during \&the simulation -\&The mu_max is used as the highest value in the distribution graph. +\&The value of \fB \-mumax\fR is used as the highest value in the distribution graph. -\&Furthermore the dipole autocorrelation function will be computed when -\&option \-corr is used. The output file name is given with the \fB \-c\fR +\&Furthermore, the dipole autocorrelation function will be computed when +\&option \fB \-corr\fR is used. The output file name is given with the \fB \-c\fR \&option. \&The correlation functions can be averaged over all molecules \&(\fB mol\fR), plotted per molecule separately (\fB molsep\fR) @@ -81,7 +81,7 @@ g_dipoles - computes the total dipole plus fluctuations \&Option \fB \-g\fR produces a plot of the distance dependent Kirkwood \&G\-factor, as well as the average cosine of the angle between the dipoles \&as a function of the distance. The plot also includes gOO and hOO -\&according to Nymand & Linse, JCP 112 (2000) pp 6386\-6395. In the same plot +\&according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386\-6395. In the same plot, \&we also include the energy per scale computed by taking the inner product of \&the dipoles divided by the distance to the third power. @@ -92,14 +92,14 @@ g_dipoles - computes the total dipole plus fluctuations \&EXAMPLES -\&g_dipoles \-corr mol \-P1 \-o dip_sqr \-mu 2.273 \-mumax 5.0 \-nofft +\&\fB g_dipoles \-corr mol \-P1 \-o dip_sqr \-mu 2.273 \-mumax 5.0 \-nofft\fR \&This will calculate the autocorrelation function of the molecular \&dipoles using a first order Legendre polynomial of the angle of the \&dipole vector and itself a time t later. For this calculation 1001 -\&frames will be used. Further the dielectric constant will be calculated -\&using an epsilonRF of infinity (default), temperature of 300 K (default) and +\&frames will be used. Further, the dielectric constant will be calculated +\&using an [GRK]epsilon[grk]RF of infinity (default), temperature of 300 K (default) and \&an average dipole moment of the molecule of 2.273 (SPC). For the \&distribution function a maximum of 5.0 will be used. .SH FILES @@ -187,7 +187,7 @@ g_dipoles - computes the total dipole plus fluctuations Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -211,10 +211,10 @@ g_dipoles - computes the total dipole plus fluctuations Correlation function to calculate: \fB none\fR, \fB mol\fR, \fB molsep\fR or \fB total\fR .BI "\-[no]pairs" "yes " - Calculate |cos theta| between all pairs of molecules. May be slow + Calculate |cos [GRK]theta[grk]| between all pairs of molecules. May be slow .BI "\-ncos" " int" " 1" - Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the \-gkr flag. + Must be 1 or 2. Determines whether the cos is computed between all molecules in one group, or between molecules in two different groups. This turns on the \fB \-gkr\fR flag. .BI "\-axis" " string" " Z" Take the normal on the computational box in direction X, Y or Z. @@ -229,16 +229,16 @@ g_dipoles - computes the total dipole plus fluctuations Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules .BI "\-rcmax" " real" " 0 " - Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used. + Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used. .BI "\-[no]phi" "no " - Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the xpm file from the \-cmap option. By default the cosine of the angle between the dipoles is plotted. + Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the \fB .xpm\fR file from the \fB \-cmap\fR option. By default the cosine of the angle between the dipoles is plotted. .BI "\-nlevels" " int" " 20" Number of colors in the cmap output .BI "\-ndegrees" " int" " 90" - Number of divisions on the y\-axis in the camp output (for 180 degrees) + Number of divisions on the \fI y\fR\-axis in the cmap output (for 180 degrees) .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames @@ -250,7 +250,7 @@ g_dipoles - computes the total dipole plus fluctuations Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_disre.1 b/man/man1/g_disre.1 index 820456eb27..9aec1eb521 100644 --- a/man/man1/g_disre.1 +++ b/man/man1/g_disre.1 @@ -1,8 +1,8 @@ -.TH g_disre 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_disre - analyzes distance restraints -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_disre\fP .BI "\-s" " topol.tpr " @@ -30,9 +30,9 @@ g_disre - analyzes distance restraints .BI "\-nlevels" " int " .BI "\-[no]third" "" .SH DESCRIPTION -\&g_disre computes violations of distance restraints. -\&If necessary all protons can be added to a protein molecule -\&using the protonate program. +\&\fB g_disre\fR computes violations of distance restraints. +\&If necessary, all protons can be added to a protein molecule +\&using the \fB g_protonate\fR program. \&The program always @@ -46,7 +46,7 @@ g_disre - analyzes distance restraints \&printing. -\&When the optional\fB \-q\fR flag is given a pdb file coloured by the +\&When the optional \fB \-q\fR flag is given a \fB .pdb\fR file coloured by the \&amount of average violations. @@ -124,7 +124,7 @@ g_disre - analyzes distance restraints Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_dist.1 b/man/man1/g_dist.1 index f39ad40e90..95a34a456c 100644 --- a/man/man1/g_dist.1 +++ b/man/man1/g_dist.1 @@ -1,8 +1,8 @@ -.TH g_dist 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_dist - calculates the distances between the centers of mass of two groups -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_dist\fP .BI "\-f" " traj.xtc " @@ -19,9 +19,9 @@ g_dist - calculates the distances between the centers of mass of two groups .BI "\-xvg" " enum " .BI "\-dist" " real " .SH DESCRIPTION -\&g_dist can calculate the distance between the centers of mass of two +\&\fB g_dist\fR can calculate the distance between the centers of mass of two \&groups of atoms as a function of time. The total distance and its -\&x, y and z components are plotted. +\&\fI x\fR\-, \fI y\fR\-, and \fI z\fR\-components are plotted. \&Or when \fB \-dist\fR is set, print all the atoms in group 2 that are diff --git a/man/man1/g_dyndom.1 b/man/man1/g_dyndom.1 index 1b0668caae..577fde8064 100644 --- a/man/man1/g_dyndom.1 +++ b/man/man1/g_dyndom.1 @@ -1,8 +1,8 @@ -.TH g_dyndom 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_dyndom - interpolate and extrapolate structure rotations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_dyndom\fP .BI "\-f" " dyndom.pdb " @@ -19,11 +19,11 @@ g_dyndom - interpolate and extrapolate structure rotations .BI "\-head" " vector " .BI "\-tail" " vector " .SH DESCRIPTION -\&g_dyndom reads a pdb file output from DynDom -\&http://www.cmp.uea.ac.uk/dyndom/ -\&It reads the coordinates, and the coordinates of the rotation axis -\&furthermore it reads an index file containing the domains. -\&Furthermore it takes the first and last atom of the arrow file +\&\fB g_dyndom\fR reads a \fB .pdb\fR file output from DynDom +\&(http://www.cmp.uea.ac.uk/dyndom/). +\&It reads the coordinates, the coordinates of the rotation axis, +\&and an index file containing the domains. +\&Furthermore, it takes the first and last atom of the arrow file \&as command line arguments (head and tail) and \&finally it takes the translation vector (given in DynDom info file) \&and the angle of rotation (also as command line arguments). If the angle @@ -75,7 +75,7 @@ g_dyndom - interpolate and extrapolate structure rotations DymDom dtermined angle of rotation about rotation vector .BI "\-trans" " real" " 0 " - Translation (Aangstroem) along rotation vector (see DynDom info file) + Translation (Angstrom) along rotation vector (see DynDom info file) .BI "\-head" " vector" " 0 0 0" First atom of the arrow vector diff --git a/man/man1/g_enemat.1 b/man/man1/g_enemat.1 index 2d03501c8d..6f638ee221 100644 --- a/man/man1/g_enemat.1 +++ b/man/man1/g_enemat.1 @@ -1,8 +1,8 @@ -.TH g_enemat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_enemat - extracts an energy matrix from an energy file -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_enemat\fP .BI "\-f" " ener.edr " @@ -35,12 +35,12 @@ g_enemat - extracts an energy matrix from an energy file .BI "\-[no]free" "" .BI "\-temp" " real " .SH DESCRIPTION -\&g_enemat extracts an energy matrix from the energy file (\fB \-f\fR). +\&\fB g_enemat\fR extracts an energy matrix from the energy file (\fB \-f\fR). \&With \fB \-groups\fR a file must be supplied with on each \&line a group of atoms to be used. For these groups matrix of \&interaction energies will be extracted from the energy file \&by looking for energy groups with names corresponding to pairs -\&of groups of atoms. E.g. if your \fB \-groups\fR file contains: +\&of groups of atoms, e.g. if your \fB \-groups\fR file contains: \&\fB 2\fR @@ -110,7 +110,7 @@ g_enemat - extracts an energy matrix from an energy file Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -122,7 +122,7 @@ g_enemat - extracts an energy matrix from an energy file Skip number of frames between data points .BI "\-[no]mean" "yes " - with \-groups extracts matrix of mean energies instead of matrix for each timestep + with \fB \-groups\fR extracts matrix of mean energies instead of matrix for each timestep .BI "\-nlevels" " int" " 20" number of levels for matrix colors diff --git a/man/man1/g_energy.1 b/man/man1/g_energy.1 index dcec1def74..617df4e23f 100644 --- a/man/man1/g_energy.1 +++ b/man/man1/g_energy.1 @@ -1,8 +1,8 @@ -.TH g_energy 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_energy - writes energies to xvg files and displays averages -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_energy\fP .BI "\-f" " ener.edr " @@ -20,6 +20,7 @@ g_energy - writes energies to xvg files and displays averages .BI "\-corr" " enecorr.xvg " .BI "\-vis" " visco.xvg " .BI "\-ravg" " runavgdf.xvg " +.BI "\-odh" " dhdl.xvg " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " @@ -38,7 +39,6 @@ g_energy - writes energies to xvg files and displays averages .BI "\-skip" " int " .BI "\-[no]aver" "" .BI "\-nmol" " int " -.BI "\-nconstr" " int " .BI "\-[no]fluc" "" .BI "\-[no]orinst" "" .BI "\-[no]ovec" "" @@ -50,56 +50,28 @@ g_energy - writes energies to xvg files and displays averages .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_energy extracts energy components or distance restraint +\&\fB g_energy\fR extracts energy components or distance restraint \&data from an energy file. The user is prompted to interactively -\&select the energy terms she wants. +\&select the desired energy terms. -\&Average, RMSD and drift are calculated with full precision from the +\&Average, RMSD, and drift are calculated with full precision from the \&simulation (see printed manual). Drift is calculated by performing -\&a LSQ fit of the data to a straight line. The reported total drift +\&a least\-squares fit of the data to a straight line. The reported total drift \&is the difference of the fit at the first and last point. \&An error estimate of the average is given based on a block averages -\&over 5 blocks using the full precision averages. The error estimate +\&over 5 blocks using the full\-precision averages. The error estimate \&can be performed over multiple block lengths with the options \&\fB \-nbmin\fR and \fB \-nbmax\fR. -\&Note that in most cases the energy files contains averages over all +\&\fB Note\fR that in most cases the energy files contains averages over all \&MD steps, or over many more points than the number of frames in -\&energy file. This makes the g_energy statistics output more accurate -\&than the xvg output. When exact averages are not present in the energy -\&file the statistics mentioned above is simply over the single, per\-frame +\&energy file. This makes the \fB g_energy\fR statistics output more accurate +\&than the \fB .xvg\fR output. When exact averages are not present in the energy +\&file, the statistics mentioned above are simply over the single, per\-frame \&energy values. -\&The term fluctuation gives the RMSD around the LSQ fit. - - -\&Some fluctuation\-dependent properties can be calculated provided -\&the correct energy terms are selected. The following properties -\&will be computed: - -\&Property Energy terms needed - -\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- - -\&Heat capacity Cp (NPT sims): Enthalpy, Temp - -\&Heat capacity Cv (NVT sims): Etot, Temp - -\&Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp - -\&Isothermal compressibility: Vol, Temp - -\&Adiabatic bulk modulus: Vol, Temp - -\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- - -\&You always need to set the number of molecules \fB \-nmol\fR, and, -\&if you used constraints in your simulations you will need to give -\&the number of constraints per molecule \fB \-nconstr\fR in order to -\&correct for this: (nconstr/2) kB is subtracted from the heat -\&capacity in this case. For instance in the case of rigid water -\&you need to give the value 3 to this option. +\&The term fluctuation gives the RMSD around the least\-squares fit. \&When the \fB \-viol\fR option is set, the time averaged @@ -129,12 +101,17 @@ g_energy - writes energies to xvg files and displays averages \&\fB \-ovec\fR also the eigenvectors are plotted. +\&Option \fB \-odh\fR extracts and plots the free energy data +\&(Hamiltoian differences and/or the Hamiltonian derivative dhdl) +\&from the \fB ener.edr\fR file. + + \&With \fB \-fee\fR an estimate is calculated for the free\-energy \&difference with an ideal gas state: -\& Delta A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT) +\& [GRK]Delta[grk] A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT) -\& Delta G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT) +\& [GRK]Delta[grk] G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT) \&where k is Boltzmann's constant, T is set by \fB \-fetemp\fR and \&the average is over the ensemble (or time in a trajectory). @@ -143,17 +120,18 @@ g_energy - writes energies to xvg files and displays averages \&and using the potential energy. This also allows for an entropy \&estimate using: -\& Delta S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- Delta A)/T +\& [GRK]Delta[grk] S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- [GRK]Delta[grk] A)/T -\& Delta S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- Delta G)/T +\& [GRK]Delta[grk] S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- [GRK]Delta[grk] G)/T \& \&When a second energy file is specified (\fB \-f2\fR), a free energy \&difference is calculated dF = \-kT ln e \-(EB\-EA)/kT A , \&where EA and EB are the energies from the first and second energy -\&files, and the average is over the ensemble A. \fB NOTE\fR that -\&the energies must both be calculated from the same trajectory. +\&files, and the average is over the ensemble A. The running average +\&of the free energy difference is printed to a file specified by \fB \-ravg\fR. +\&\fB Note\fR that the energies must both be calculated from the same trajectory. .SH FILES .BI "\-f" " ener.edr" .B Input @@ -215,6 +193,10 @@ g_energy - writes energies to xvg files and displays averages .B Output, Opt. xvgr/xmgr file +.BI "\-odh" " dhdl.xvg" +.B Output, Opt. + xvgr/xmgr file + .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit @@ -232,7 +214,7 @@ g_energy - writes energies to xvg files and displays averages Last frame (ps) to read from trajectory .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -270,9 +252,6 @@ g_energy - writes energies to xvg files and displays averages .BI "\-nmol" " int" " 1" Number of molecules in your sample: the energies are divided by this number -.BI "\-nconstr" " int" " 0" - Number of constraints per molecule. Necessary for calculating the heat capacity - .BI "\-[no]fluc" "no " Calculate autocorrelation of energy fluctuations rather than energy itself @@ -280,7 +259,7 @@ g_energy - writes energies to xvg files and displays averages Analyse instantaneous orientation data .BI "\-[no]ovec" "no " - Also plot the eigenvectors with \-oten + Also plot the eigenvectors with \fB \-oten\fR .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames @@ -292,7 +271,7 @@ g_energy - writes energies to xvg files and displays averages Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_filter.1 b/man/man1/g_filter.1 index 02ebe01497..c662bef582 100644 --- a/man/man1/g_filter.1 +++ b/man/man1/g_filter.1 @@ -1,8 +1,8 @@ -.TH g_filter 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_filter - frequency filters trajectories, useful for making smooth movies -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_filter\fP .BI "\-f" " traj.xtc " @@ -22,8 +22,8 @@ g_filter - frequency filters trajectories, useful for making smooth movies .BI "\-[no]nojump" "" .BI "\-[no]fit" "" .SH DESCRIPTION -\&g_filter performs frequency filtering on a trajectory. -\&The filter shape is cos(pi t/A) + 1 from \-A to +A, where A is given +\&\fB g_filter\fR performs frequency filtering on a trajectory. +\&The filter shape is cos([GRK]pi[grk] t/A) + 1 from \-A to +A, where A is given \&by the option \fB \-nf\fR times the time step in the input trajectory. \&This filter reduces fluctuations with period A by 85%, with period \&2*A by 50% and with period 3*A by 17% for low\-pass filtering. @@ -31,7 +31,7 @@ g_filter - frequency filters trajectories, useful for making smooth movies \&Option \fB \-ol\fR writes a low\-pass filtered trajectory. -\&A frame is written every \fB nf\fR input frames. +\&A frame is written every \fB \-nf\fR input frames. \&This ratio of filter length and output interval ensures a good \&suppression of aliasing of high\-frequency motion, which is useful for \&making smooth movies. Also averages of properties which are linear @@ -43,7 +43,7 @@ g_filter - frequency filters trajectories, useful for making smooth movies \&Option \fB \-oh\fR writes a high\-pass filtered trajectory. \&The high\-pass filtered coordinates are added to the coordinates \&from the structure file. When using high\-pass filtering use \fB \-fit\fR -\&or make sure you use a trajectory which has been fitted on +\&or make sure you use a trajectory that has been fitted on \&the coordinates in the structure file. .SH FILES .BI "\-f" " traj.xtc" @@ -86,7 +86,7 @@ g_filter - frequency filters trajectories, useful for making smooth movies Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-nf" " int" " 10" Sets the filter length as well as the output interval for low\-pass filtering diff --git a/man/man1/g_gyrate.1 b/man/man1/g_gyrate.1 index 20dbf17268..ef57f01582 100644 --- a/man/man1/g_gyrate.1 +++ b/man/man1/g_gyrate.1 @@ -1,8 +1,8 @@ -.TH g_gyrate 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_gyrate - calculates the radius of gyration -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_gyrate\fP .BI "\-f" " traj.xtc " @@ -31,8 +31,8 @@ g_gyrate - calculates the radius of gyration .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_gyrate computes the radius of gyration of a group of atoms -\&and the radii of gyration about the x, y and z axes, +\&\fB g_gyrate\fR computes the radius of gyration of a group of atoms +\&and the radii of gyration about the \fI x\fR\-, \fI y\fR\- and \fI z\fR\-axes, \&as a function of time. The atoms are explicitly mass weighted. @@ -41,8 +41,8 @@ g_gyrate - calculates the radius of gyration \&sized parts. -\&With the option \fB \-nz\fR 2D radii of gyration in the x\-y plane -\&of slices along the z\-axis are calculated. +\&With the option \fB \-nz\fR 2D radii of gyration in the \fI x\-y\fR plane +\&of slices along the \fI z\fR\-axis are calculated. .SH FILES .BI "\-f" " traj.xtc" .B Input @@ -84,7 +84,7 @@ g_gyrate - calculates the radius of gyration Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -114,7 +114,7 @@ g_gyrate - calculates the radius of gyration Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_h2order.1 b/man/man1/g_h2order.1 index 2349dae743..7295c29307 100644 --- a/man/man1/g_h2order.1 +++ b/man/man1/g_h2order.1 @@ -1,8 +1,8 @@ -.TH g_h2order 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_h2order - computes the orientation of water molecules -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_h2order\fP .BI "\-f" " traj.xtc " @@ -21,12 +21,12 @@ g_h2order - computes the orientation of water molecules .BI "\-d" " string " .BI "\-sl" " int " .SH DESCRIPTION -\&Compute the orientation of water molecules with respect to the normal +\&\fB g_h2order\fR computes the orientation of water molecules with respect to the normal \&of the box. The program determines the average cosine of the angle -\&between de dipole moment of water and an axis of the box. The box is +\&between the dipole moment of water and an axis of the box. The box is \÷d in slices and the average orientation per slice is printed. \&Each water molecule is assigned to a slice, per time frame, based on the -\&position of the oxygen. When \-nm is used the angle between the water +\&position of the oxygen. When \fB \-nm\fR is used, the angle between the water \&dipole and the axis from the center of mass to the oxygen is calculated \&instead of the angle between the dipole and a box axis. .SH FILES @@ -70,7 +70,7 @@ g_h2order - computes the orientation of water molecules Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -82,7 +82,7 @@ g_h2order - computes the orientation of water molecules Calculate order parameter as function of boxlength, dividing the box in nr slices. .SH KNOWN PROBLEMS -\- The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different. +\- The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different. .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_hbond.1 b/man/man1/g_hbond.1 index 049b54d1d6..9f1b3f5a93 100644 --- a/man/man1/g_hbond.1 +++ b/man/man1/g_hbond.1 @@ -1,8 +1,8 @@ -.TH g_hbond 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_hbond - computes and analyzes hydrogen bonds -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_hbond\fP .BI "\-f" " traj.xtc " @@ -26,6 +26,7 @@ g_hbond - computes and analyzes hydrogen bonds .BI "\-b" " time " .BI "\-e" " time " .BI "\-dt" " time " +.BI "\-tu" " enum " .BI "\-xvg" " enum " .BI "\-a" " real " .BI "\-r" " real " @@ -53,7 +54,7 @@ g_hbond - computes and analyzes hydrogen bonds .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are +\&\fB g_hbond\fR computes and analyzes hydrogen bonds. Hydrogen bonds are \&determined based on cutoffs for the angle Acceptor \- Donor \- Hydrogen \&(zero is extended) and the distance Hydrogen \- Acceptor. \&OH and NH groups are regarded as donors, O is an acceptor always, @@ -67,7 +68,7 @@ g_hbond - computes and analyzes hydrogen bonds \&groups are analyzed. -\&If you set \-shell, you will be asked for an additional index group +\&If you set \fB \-shell\fR, you will be asked for an additional index group \&which should contain exactly one atom. In this case, only hydrogen \&bonds between atoms within the shell distance from the one atom are \&considered. @@ -205,6 +206,9 @@ g_hbond - computes and analyzes hydrogen bonds .BI "\-dt" " time" " 0 " Only use frame when t MOD dt = first time (ps) +.BI "\-tu" " enum" " ps" + Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR + .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -218,7 +222,7 @@ g_hbond - computes and analyzes hydrogen bonds Use distance Donor\-Acceptor (if TRUE) or Hydrogen\-Acceptor (FALSE) .BI "\-r2" " real" " 0 " - Second cutoff radius. Mainly useful with \-contact and \-ac + Second cutoff radius. Mainly useful with \fB \-contact\fR and \fB \-ac\fR .BI "\-abin" " real" " 1 " Binwidth angle distribution (degrees) @@ -236,19 +240,19 @@ g_hbond - computes and analyzes hydrogen bonds when 0, only calculate hydrogen bonds within nm shell around one particle .BI "\-fitstart" " real" " 1 " - Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With \-gemfit we suggest \-fitstart 0 + Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With \fB \-gemfit\fR we suggest \fB \-fitstart 0\fR .BI "\-fitstart" " real" " 1 " - Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with \-gemfit) + Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with \fB \-gemfit\fR) .BI "\-temp" " real" " 298.15" Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming .BI "\-smooth" " real" " \-1 " - If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau) + If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/[GRK]tau[grk]) .BI "\-dump" " int" " 0" - Dump the first N hydrogen bond ACFs in a single xvg file for debugging + Dump the first N hydrogen bond ACFs in a single \fB .xvg\fR file for debugging .BI "\-max_hb" " real" " 0 " Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly @@ -260,7 +264,7 @@ g_hbond - computes and analyzes hydrogen bonds Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details.: \fB none\fR, \fB dd\fR, \fB ad\fR, \fB aa\fR or \fB a4\fR .BI "\-diff" " real" " \-1 " - Dffusion coefficient to use in the rev. gem. recomb. kinetic model. If non\-positive, then it will be fitted to the ACF along with ka and kd. + Dffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd. .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames @@ -272,7 +276,7 @@ g_hbond - computes and analyzes hydrogen bonds Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_helix.1 b/man/man1/g_helix.1 index cfdd05e33e..4bacd85b44 100644 --- a/man/man1/g_helix.1 +++ b/man/man1/g_helix.1 @@ -1,8 +1,8 @@ -.TH g_helix 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_helix - calculates basic properties of alpha helices -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_helix\fP .BI "\-s" " topol.tpr " @@ -27,46 +27,46 @@ g_helix - calculates basic properties of alpha helices .BI "\-ahxstart" " int " .BI "\-ahxend" " int " .SH DESCRIPTION -\&g_helix computes all kind of helix properties. First, the peptide -\&is checked to find the longest helical part. This is determined by -\&Hydrogen bonds and Phi/Psi angles. +\&\fB g_helix\fR computes all kinds of helix properties. First, the peptide +\&is checked to find the longest helical part, as determined by +\&hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles. \&That bit is fitted -\&to an ideal helix around the Z\-axis and centered around the origin. +\&to an ideal helix around the \fI z\fR\-axis and centered around the origin. \&Then the following properties are computed: -\&\fB 1.\fR Helix radius (file radius.xvg). This is merely the -\&RMS deviation in two dimensions for all Calpha atoms. +\&\fB 1.\fR Helix radius (file \fB radius.xvg\fR). This is merely the +\&RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms. \&it is calced as sqrt((SUM i(x2(i)+y2(i)))/N), where N is the number \&of backbone atoms. For an ideal helix the radius is 0.23 nm -\&\fB 2.\fR Twist (file twist.xvg). The average helical angle per -\&residue is calculated. For alpha helix it is 100 degrees, -\&for 3\-10 helices it will be smaller, +\&\fB 2.\fR Twist (file \fB twist.xvg\fR). The average helical angle per +\&residue is calculated. For an [GRK]alpha[grk]\-helix it is 100 degrees, +\&for 3\-10 helices it will be smaller, and \&for 5\-helices it will be larger. -\&\fB 3.\fR Rise per residue (file rise.xvg). The helical rise per -\&residue is plotted as the difference in Z\-coordinate between Ca -\&atoms. For an ideal helix this is 0.15 nm +\&\fB 3.\fR Rise per residue (file \fB rise.xvg\fR). The helical rise per +\&residue is plotted as the difference in \fI z\fR\-coordinate between C[GRK]alpha[grk] +\&atoms. For an ideal helix, this is 0.15 nm -\&\fB 4.\fR Total helix length (file len\-ahx.xvg). The total length +\&\fB 4.\fR Total helix length (file \fB len\-ahx.xvg\fR). The total length \&of the \&helix in nm. This is simply the average rise (see above) times the \&number of helical residues (see below). -\&\fB 5.\fR Number of helical residues (file n\-ahx.xvg). The title says +\&\fB 5.\fR Number of helical residues (file \fB n\-ahx.xvg\fR). The title says \&it all. -\&\fB 6.\fR Helix Dipole, backbone only (file dip\-ahx.xvg). +\&\fB 6.\fR Helix dipole, backbone only (file \fB dip\-ahx.xvg\fR). -\&\fB 7.\fR RMS deviation from ideal helix, calculated for the Calpha -\&atoms only (file rms\-ahx.xvg). +\&\fB 7.\fR RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk] +\&atoms only (file \fB rms\-ahx.xvg\fR). -\&\fB 8.\fR Average Calpha\-Calpha dihedral angle (file phi\-ahx.xvg). +\&\fB 8.\fR Average C[GRK]alpha[grk] \- C[GRK]alpha[grk] dihedral angle (file \fB phi\-ahx.xvg\fR). -\&\fB 9.\fR Average Phi and Psi angles (file phipsi.xvg). +\&\fB 9.\fR Average [GRK]phi[grk] and [GRK]psi[grk] angles (file \fB phipsi.xvg\fR). -\&\fB 10.\fR Ellipticity at 222 nm according to \fI Hirst and Brooks\fR +\&\fB 10.\fR Ellipticity at 222 nm according to Hirst and Brooks. \& @@ -115,7 +115,7 @@ g_helix - calculates basic properties of alpha helices Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-r0" " int" " 1" The first residue number in the sequence diff --git a/man/man1/g_helixorient.1 b/man/man1/g_helixorient.1 index c6a142971b..6bcc4df1df 100644 --- a/man/man1/g_helixorient.1 +++ b/man/man1/g_helixorient.1 @@ -1,8 +1,8 @@ -.TH g_helixorient 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_helixorient - calculates local pitch/bending/rotation/orientation inside helices -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_helixorient\fP .BI "\-s" " topol.tpr " @@ -26,30 +26,30 @@ g_helixorient - calculates local pitch/bending/rotation/orientation inside helic .BI "\-[no]sidechain" "" .BI "\-[no]incremental" "" .SH DESCRIPTION -\&g_helixorient calculates the coordinates and direction of the average +\&\fB g_helixorient\fR calculates the coordinates and direction of the average \&axis inside an alpha helix, and the direction/vectors of both the -\&alpha carbon and (optionally) a sidechain atom relative to the axis. +\&C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis. -\&As input, you need to specify an index group with alpha carbon atoms -\&corresponding to an alpha helix of continuous residues. Sidechain +\&As input, you need to specify an index group with C[GRK]alpha[grk] atoms +\&corresponding to an [GRK]alpha[grk]\-helix of continuous residues. Sidechain \&directions require a second index group of the same size, containing \&the heavy atom in each residue that should represent the sidechain. -\&Note that this program does not do any fitting of structures. +\&\fB Note\fR that this program does not do any fitting of structures. -\&We need four Calpha coordinates to define the local direction of the helix +\&We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix \&axis. \&The tilt/rotation is calculated from Euler rotations, where we define -\&the helix axis as the local X axis, the residues/CA\-vector as Y, and the -\&Z axis from their cross product. We use the Euler Y\-Z\-X rotation, meaning +\&the helix axis as the local \fI x\fR\-axis, the residues/C[GRK]alpha[grk] vector as \fI y\fR, and the +\&\fI z\fR\-axis from their cross product. We use the Euler Y\-Z\-X rotation, meaning \&we first tilt the helix axis (1) around and (2) orthogonal to the residues \&vector, and finally apply the (3) rotation around it. For debugging or other -\&purposes, we also write out the actual Euler rotation angles as theta1\-3.xvg +\&purposes, we also write out the actual Euler rotation angles as \fB theta[1\-3].xvg\fR .SH FILES .BI "\-s" " topol.tpr" .B Input diff --git a/man/man1/g_lie.1 b/man/man1/g_lie.1 index 8596ace2b9..18405a3ba3 100644 --- a/man/man1/g_lie.1 +++ b/man/man1/g_lie.1 @@ -1,8 +1,8 @@ -.TH g_lie 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_lie - free energy estimate from linear combinations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_lie\fP .BI "\-f" " ener.edr " @@ -21,7 +21,7 @@ g_lie - free energy estimate from linear combinations .BI "\-Cqq" " real " .BI "\-ligand" " string " .SH DESCRIPTION -\&g_lie computes a free energy estimate based on an energy analysis +\&\fB g_lie\fR computes a free energy estimate based on an energy analysis \&from. One needs an energy file with the following components: \&Coul (A\-B) LJ\-SR (A\-B) etc. .SH FILES @@ -53,7 +53,7 @@ g_lie - free energy estimate from linear combinations Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_mdmat.1 b/man/man1/g_mdmat.1 index 5ecc49f203..49be8f0cf5 100644 --- a/man/man1/g_mdmat.1 +++ b/man/man1/g_mdmat.1 @@ -1,8 +1,8 @@ -.TH g_mdmat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_mdmat - calculates residue contact maps -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_mdmat\fP .BI "\-f" " traj.xtc " @@ -21,16 +21,15 @@ g_mdmat - calculates residue contact maps .BI "\-t" " real " .BI "\-nlevels" " int " .SH DESCRIPTION -\&g_mdmat makes distance matrices consisting of the smallest distance -\&between residue pairs. With \-frames these distance matrices can be -\&stored as a function -\&of time, to be able to see differences in tertiary structure as a -\&funcion of time. If you choose your options unwise, this may generate -\&a large output file. Default only an averaged matrix over the whole +\&\fB g_mdmat\fR makes distance matrices consisting of the smallest distance +\&between residue pairs. With \fB \-frames\fR, these distance matrices can be +\&stored in order to see differences in tertiary structure as a +\&function of time. If you choose your options unwisely, this may generate +\&a large output file. By default, only an averaged matrix over the whole \&trajectory is output. \&Also a count of the number of different atomic contacts between \&residues over the whole trajectory can be made. -\&The output can be processed with xpm2ps to make a PostScript (tm) plot. +\&The output can be processed with \fB xpm2ps\fR to make a PostScript (tm) plot. .SH FILES .BI "\-f" " traj.xtc" .B Input diff --git a/man/man1/g_membed.1 b/man/man1/g_membed.1 index 659033e215..5cf08d2aa8 100644 --- a/man/man1/g_membed.1 +++ b/man/man1/g_membed.1 @@ -1,8 +1,8 @@ -.TH g_membed 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_membed - embeds a protein into a lipid bilayer -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_membed\fP .BI "\-f" " into_mem.tpr " @@ -39,6 +39,7 @@ g_membed - embeds a protein into a lipid bilayer .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " +.BI "\-multidir" " rundir " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " @@ -58,28 +59,27 @@ g_membed - embeds a protein into a lipid bilayer .BI "\-[no]compact" "" .BI "\-[no]v" "" .SH DESCRIPTION -\&g_membed embeds a membrane protein into an equilibrated lipid bilayer at the position +\&\fB g_membed\fR embeds a membrane protein into an equilibrated lipid bilayer at the position \&and orientation specified by the user. -\& \&SHORT MANUAL \-\-\-\-\-\-\-\-\-\-\-\- \&The user should merge the structure files of the protein and membrane (+solvent), creating a \&single structure file with the protein overlapping the membrane at the desired position and -\&orientation. Box size should be taken from the membrane structure file. The corresponding topology -\&files should also be merged. Consecutively, create a tpr file (input for g_membed) from these files,with the following options included in the mdp file. +\&orientation. The box size is taken from the membrane structure file. The corresponding topology +\&files should also be merged. Consecutively, create a \fB .tpr\fR file (input for \fB g_membed\fR) from these files,with the following options included in the \fB .mdp\fR file. -\& \- integrator = md +\& \- \fB integrator = md\fR -\& \- energygrp = Protein (or other group that you want to insert) +\& \- \fB energygrp = Protein\fR (or other group that you want to insert) -\& \- freezegrps = Protein +\& \- \fB freezegrps = Protein\fR -\& \- freezedim = Y Y Y +\& \- \fB freezedim = Y Y Y\fR -\& \- energygrp_excl = Protein Protein +\& \- \fB energygrp_excl = Protein Protein\fR \&The output is a structure file containing the protein embedded in the membrane. If a topology \&file is provided, the number of lipid and @@ -87,33 +87,31 @@ g_membed - embeds a protein into a lipid bilayer \&For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169\-2174, Appendix. -\& \&SHORT METHOD DESCRIPTION \&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- -\&1. The protein is resized around its center of mass by a factor \-xy in the xy\-plane -\&(the membrane plane) and a factor \-z in the z\-direction (if the size of the +\&1. The protein is resized around its center of mass by a factor \fB \-xy\fR in the xy\-plane +\&(the membrane plane) and a factor \fB \-z\fR in the \fI z\fR\-direction (if the size of the \&protein in the z\-direction is the same or smaller than the width of the membrane, a -\&\-z value larger than 1 can prevent that the protein will be enveloped by the lipids). +\&\fB \-z\fR value larger than 1 can prevent that the protein will be enveloped by the lipids). \&2. All lipid and solvent molecules overlapping with the resized protein are removed. All -\&intraprotein interactions are turned off to prevent numerical issues for small values of \-xy -\& or \-z +\&intraprotein interactions are turned off to prevent numerical issues for small values of \fB \-xy\fR +\& or \fB \-z\fR \&3. One md step is performed. -\&4. The resize factor (\-xy or \-z) is incremented by a small amount ((1\-xy)/nxy or (1\-z)/nz) and the +\&4. The resize factor (\fB \-xy\fR or \fB \-z\fR) is incremented by a small amount ((1\-xy)/nxy or (1\-z)/nz) and the \&protein is resized again around its center of mass. The resize factor for the xy\-plane -\&is incremented first. The resize factor for the z\-direction is not changed until the \-xy factor -\&is 1 (thus after \-nxy iteration). +\&is incremented first. The resize factor for the z\-direction is not changed until the \fB \-xy\fR factor +\&is 1 (thus after \fB \-nxy\fR iterations). -\&5. Repeat step 3 and 4 until the protein reaches its original size (\-nxy + \-nz iterations). +\&5. Repeat step 3 and 4 until the protein reaches its original size (\fB \-nxy\fR + \fB \-nz\fR iterations). -\&For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169\-2174. +\&For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169\-2174. -\& \&NOTE \-\-\-\- @@ -121,10 +119,9 @@ g_membed - embeds a protein into a lipid bilayer \& \- Protein can be any molecule you want to insert in the membrane. \& \- It is recommended to perform a short equilibration run after the embedding -\&(see Wolf et al, J Comp Chem 31 (2010) 2169\-2174, to re\-equilibrate the membrane. Clearly +\&(see Wolf et al, J Comp Chem 31 (2010) 2169\-2174), to re\-equilibrate the membrane. Clearly \&protein equilibration might require longer. -\& .SH FILES .BI "\-f" " into_mem.tpr" @@ -263,6 +260,10 @@ g_membed - embeds a protein into a lipid bilayer .B Output, Opt. Index file +.BI "\-multidir" " rundir" +.B Input, Opt., Mult. + Run directory + .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit diff --git a/man/man1/g_mindist.1 b/man/man1/g_mindist.1 index 67428bd687..28827102f2 100644 --- a/man/man1/g_mindist.1 +++ b/man/man1/g_mindist.1 @@ -1,8 +1,8 @@ -.TH g_mindist 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_mindist - calculates the minimum distance between two groups -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_mindist\fP .BI "\-f" " traj.xtc " @@ -33,7 +33,7 @@ g_mindist - calculates the minimum distance between two groups .BI "\-[no]respertime" "" .BI "\-[no]printresname" "" .SH DESCRIPTION -\&g_mindist computes the distance between one group and a number of +\&\fB g_mindist\fR computes the distance between one group and a number of \&other groups. Both the minimum distance \&(between any pair of atoms from the respective groups) \&and the number of contacts within a given @@ -111,7 +111,7 @@ g_mindist - calculates the minimum distance between two groups Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_morph.1 b/man/man1/g_morph.1 index e55da0d936..d98312babf 100644 --- a/man/man1/g_morph.1 +++ b/man/man1/g_morph.1 @@ -1,8 +1,8 @@ -.TH g_morph 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_morph - linear interpolation of conformations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_morph\fP .BI "\-f1" " conf1.gro " @@ -20,15 +20,15 @@ g_morph - linear interpolation of conformations .BI "\-last" " real " .BI "\-[no]fit" "" .SH DESCRIPTION -\&g_morph does a linear interpolation of conformations in order to +\&\fB g_morph\fR does a linear interpolation of conformations in order to \&create intermediates. Of course these are completely unphysical, but \&that you may try to justify yourself. Output is in the form of a \&generic trajectory. The number of intermediates can be controlled with -\&the \-ninterm flag. The first and last flag correspond to the way of +\&the \fB \-ninterm\fR flag. The first and last flag correspond to the way of \&interpolating: 0 corresponds to input structure 1 while \&1 corresponds to input structure 2. -\&If you specify first 0 or last 1 extrapolation will be -\&on the path from input structure x1 to x2. In general the coordinates +\&If you specify \fB \-first\fR 0 or \fB \-last\fR 1 extrapolation will be +\&on the path from input structure x1 to x2. In general, the coordinates \&of the intermediate x(i) out of N total intermidates correspond to: @@ -36,8 +36,8 @@ g_morph - linear interpolation of conformations \&Finally the RMSD with respect to both input structures can be computed -\&if explicitly selected (\-or option). In that case an index file may be -\&read to select what group RMS is computed from. +\&if explicitly selected (\fB \-or\fR option). In that case, an index file may be +\&read to select the group from which the RMS is computed. .SH FILES .BI "\-f1" " conf1.gro" .B Input @@ -70,7 +70,7 @@ g_morph - linear interpolation of conformations Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_msd.1 b/man/man1/g_msd.1 index 838ba4cc62..d6ba62758c 100644 --- a/man/man1/g_msd.1 +++ b/man/man1/g_msd.1 @@ -1,8 +1,8 @@ -.TH g_msd 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_msd - calculates mean square displacements -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_msd\fP .BI "\-f" " traj.xtc " @@ -30,7 +30,7 @@ g_msd - calculates mean square displacements .BI "\-beginfit" " time " .BI "\-endfit" " time " .SH DESCRIPTION -\&g_msd computes the mean square displacement (MSD) of atoms from +\&\fB g_msd\fR computes the mean square displacement (MSD) of atoms from \&a set of initial positions. This provides an easy way to compute \&the diffusion constant using the Einstein relation. \&The time between the reference points for the MSD calculation @@ -49,7 +49,8 @@ g_msd - calculates mean square displacements \&each group, the order in the output is: trace xx yy zz yx zx zy. -\&If \fB \-mol\fR is set, g_msd plots the MSD for individual molecules: +\&If \fB \-mol\fR is set, \fB g_msd\fR plots the MSD for individual molecules +\&(including making molecules whole across periodic boundaries): \&for each individual molecule a diffusion constant is computed for \&its center of mass. The chosen index group will be split into \&molecules. @@ -62,7 +63,7 @@ g_msd - calculates mean square displacements \&With the option \fB \-rmcomm\fR, the center of mass motion of a \&specific group can be removed. For trajectories produced with \&GROMACS this is usually not necessary, -\&as mdrun usually already removes the center of mass motion. +\&as \fB mdrun\fR usually already removes the center of mass motion. \&When you use this option be sure that the whole system is stored \&in the trajectory file. @@ -79,7 +80,7 @@ g_msd - calculates mean square displacements \&\fB \-beginfit\fR and \fB \-endfit\fR. -\&Option \fB \-pdb\fR writes a pdb file with the coordinates of the frame +\&Option \fB \-pdb\fR writes a \fB .pdb\fR file with the coordinates of the frame \&at time \fB \-tpdb\fR with in the B\-factor field the square root of \&the diffusion coefficient of the molecule. \&This option implies option \fB \-mol\fR. @@ -128,7 +129,7 @@ g_msd - calculates mean square displacements Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -152,7 +153,7 @@ g_msd - calculates mean square displacements Remove center of mass motion .BI "\-tpdb" " time" " 0 " - The frame to use for option \-pdb (ps) + The frame to use for option \fB \-pdb\fR (ps) .BI "\-trestart" " time" " 10 " Time between restarting points in trajectory (ps) diff --git a/man/man1/g_nmeig.1 b/man/man1/g_nmeig.1 index 16a72bb1cb..5993d2d358 100644 --- a/man/man1/g_nmeig.1 +++ b/man/man1/g_nmeig.1 @@ -1,14 +1,15 @@ -.TH g_nmeig 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_nmeig - diagonalizes the Hessian -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_nmeig\fP .BI "\-f" " hessian.mtx " .BI "\-s" " topol.tpr " .BI "\-of" " eigenfreq.xvg " .BI "\-ol" " eigenval.xvg " +.BI "\-qc" " quant_corr.xvg " .BI "\-v" " eigenvec.trr " .BI "\-[no]h" "" .BI "\-[no]version" "" @@ -17,8 +18,10 @@ g_nmeig - diagonalizes the Hessian .BI "\-[no]m" "" .BI "\-first" " int " .BI "\-last" " int " +.BI "\-T" " real " +.BI "\-[no]constr" "" .SH DESCRIPTION -\&g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, +\&\fB g_nmeig\fR calculates the eigenvectors/values of a (Hessian) matrix, \&which can be calculated with \fB mdrun\fR. \&The eigenvectors are written to a trajectory file (\fB \-v\fR). \&The structure is written first with t=0. The eigenvectors @@ -26,9 +29,32 @@ g_nmeig - diagonalizes the Hessian \&The eigenvectors can be analyzed with \fB g_anaeig\fR. \&An ensemble of structures can be generated from the eigenvectors with \&\fB g_nmens\fR. When mass weighting is used, the generated eigenvectors -\&will be scaled back to plain cartesian coordinates before generating the -\&output \- in this case they will no longer be exactly orthogonal in the -\&standard cartesian norm (But in the mass weighted norm they would be). +\&will be scaled back to plain Cartesian coordinates before generating the +\&output. In this case, they will no longer be exactly orthogonal in the +\&standard Cartesian norm, but in the mass\-weighted norm they would be. + + +\&This program can be optionally used to compute quantum corrections to heat capacity +\&and enthalpy by providing an extra file argument \fB \-qcorr\fR. See the GROMACS +\&manual, Chapter 1, for details. The result includes subtracting a harmonic +\°ree of freedom at the given temperature. +\&The total correction is printed on the terminal screen. +\&The recommended way of getting the corrections out is: + + +\&\fB g_nmeig \-s topol.tpr \-f nm.mtx \-first 7 \-last 10000 \-T 300 \-qc [\-constr]\fR + + +\&The \fB \-constr\fR option should be used when bond constraints were used during the +\&simulation \fB for all the covalent bonds\fR. If this is not the case, +\&you need to analyze the \fB quant_corr.xvg\fR file yourself. + + +\&To make things more flexible, the program can also take virtual sites into account +\&when computing quantum corrections. When selecting \fB \-constr\fR and +\&\fB \-qc\fR, the \fB \-begin\fR and \fB \-end\fR options will be set automatically as well. +\&Again, if you think you know it better, please check the \fB eigenfreq.xvg\fR +\&output. .SH FILES .BI "\-f" " hessian.mtx" .B Input @@ -36,7 +62,7 @@ g_nmeig - diagonalizes the Hessian .BI "\-s" " topol.tpr" .B Input - Structure+mass(db): tpr tpb tpa gro g96 pdb + Run input file: tpr tpb tpa .BI "\-of" " eigenfreq.xvg" .B Output @@ -46,6 +72,10 @@ g_nmeig - diagonalizes the Hessian .B Output xvgr/xmgr file +.BI "\-qc" " quant_corr.xvg" +.B Output, Opt. + xvgr/xmgr file + .BI "\-v" " eigenvec.trr" .B Output Full precision trajectory: trr trj cpt @@ -72,6 +102,12 @@ g_nmeig - diagonalizes the Hessian .BI "\-last" " int" " 50" Last eigenvector to write away +.BI "\-T" " real" " 298.15" + Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations + +.BI "\-[no]constr" "no " + If constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to set this for computing the quantum corrections. + .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_nmens.1 b/man/man1/g_nmens.1 index 85d3f98a75..746720ecf5 100644 --- a/man/man1/g_nmens.1 +++ b/man/man1/g_nmens.1 @@ -1,8 +1,8 @@ -.TH g_nmens 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_nmens - generates an ensemble of structures from the normal modes -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_nmens\fP .BI "\-v" " eigenvec.trr " @@ -21,7 +21,7 @@ g_nmens - generates an ensemble of structures from the normal modes .BI "\-last" " int " .SH DESCRIPTION \&\fB g_nmens\fR generates an ensemble around an average structure -\&in a subspace which is defined by a set of normal modes (eigenvectors). +\&in a subspace that is defined by a set of normal modes (eigenvectors). \&The eigenvectors are assumed to be mass\-weighted. \&The position along each eigenvector is randomly taken from a Gaussian \&distribution with variance kT/eigenvalue. diff --git a/man/man1/g_nmtraj.1 b/man/man1/g_nmtraj.1 index 173fa320fa..3363316cb0 100644 --- a/man/man1/g_nmtraj.1 +++ b/man/man1/g_nmtraj.1 @@ -1,8 +1,8 @@ -.TH g_nmtraj 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_nmtraj - generate a virtual trajectory from an eigenvector -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_nmtraj\fP .BI "\-s" " topol.tpr " @@ -18,7 +18,7 @@ g_nmtraj - generate a virtual trajectory from an eigenvector .BI "\-nframes" " int " .SH DESCRIPTION \&\fB g_nmtraj\fR generates an virtual trajectory from an eigenvector, -\&corresponding to a harmonic cartesian oscillation around the average +\&corresponding to a harmonic Cartesian oscillation around the average \&structure. The eigenvectors should normally be mass\-weighted, but you can \&use non\-weighted eigenvectors to generate orthogonal motions. \&The output frames are written as a trajectory file covering an entire period, and @@ -26,10 +26,10 @@ g_nmtraj - generate a virtual trajectory from an eigenvector \&PDB format you can view it directly in PyMol and also render a photorealistic movie. \&Motion amplitudes are calculated from the eigenvalues and a preset temperature, \&assuming equipartition of the energy over all modes. To make the motion clearly visible -\&in PyMol you might want to amplify it by setting an unrealistic high temperature. -\&However, be aware that both the linear cartesian displacements and mass weighting will +\&in PyMol you might want to amplify it by setting an unrealistically high temperature. +\&However, be aware that both the linear Cartesian displacements and mass weighting will \&lead to serious structure deformation for high amplitudes \- this is is simply a limitation -\&of the cartesian normal mode model. By default the selected eigenvector is set to 7, since +\&of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since \& the first six normal modes are the translational and rotational degrees of freedom. .SH FILES .BI "\-s" " topol.tpr" diff --git a/man/man1/g_order.1 b/man/man1/g_order.1 index 8ff7a0d613..3e4267605a 100644 --- a/man/man1/g_order.1 +++ b/man/man1/g_order.1 @@ -1,8 +1,8 @@ -.TH g_order 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_order - computes the order parameter per atom for carbon tails -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_order\fP .BI "\-f" " traj.xtc " @@ -44,9 +44,9 @@ g_order - computes the order parameter per atom for carbon tails \&The program can also give all \&diagonal elements of the order tensor and even calculate the deuterium -\&order parameter Scd (default). If the option \-szonly is given, only one -\&order tensor component (specified by the \-d option) is given and the -\&order parameter per slice is calculated as well. If \-szonly is not +\&order parameter Scd (default). If the option \fB \-szonly\fR is given, only one +\&order tensor component (specified by the \fB \-d\fR option) is given and the +\&order parameter per slice is calculated as well. If \fB \-szonly\fR is not \&selected, all diagonal elements and the deuterium order parameter is \&given. @@ -125,7 +125,7 @@ The tetrahedrality order parameters can be determined Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -134,10 +134,10 @@ The tetrahedrality order parameters can be determined Direction of the normal on the membrane: \fB z\fR, \fB x\fR or \fB y\fR .BI "\-sl" " int" " 1" - Calculate order parameter as function of boxlength, dividing the box in nr slices. + Calculate order parameter as function of box length, dividing the box in nr slices. .BI "\-[no]szonly" "no " - Only give Sz element of order tensor. (axis can be specified with \-d) + Only give Sz element of order tensor. (axis can be specified with \fB \-d\fR) .BI "\-[no]unsat" "no " Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. diff --git a/man/man1/g_polystat.1 b/man/man1/g_polystat.1 index 08e6ffe940..8587c0891b 100644 --- a/man/man1/g_polystat.1 +++ b/man/man1/g_polystat.1 @@ -1,8 +1,8 @@ -.TH g_polystat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_polystat - calculates static properties of polymers -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_polystat\fP .BI "\-s" " topol.tpr " @@ -24,7 +24,7 @@ g_polystat - calculates static properties of polymers .BI "\-[no]mw" "" .BI "\-[no]pc" "" .SH DESCRIPTION -\&g_polystat plots static properties of polymers as a function of time +\&\fB g_polystat\fR plots static properties of polymers as a function of time \&and prints the average. @@ -103,7 +103,7 @@ g_polystat - calculates static properties of polymers Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_potential.1 b/man/man1/g_potential.1 index 124063e34e..6f928eeca4 100644 --- a/man/man1/g_potential.1 +++ b/man/man1/g_potential.1 @@ -1,8 +1,8 @@ -.TH g_potential 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_potential - calculates the electrostatic potential across the box -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_potential\fP .BI "\-f" " traj.xtc " @@ -28,14 +28,14 @@ g_potential - calculates the electrostatic potential across the box .BI "\-ng" " int " .BI "\-[no]correct" "" .SH DESCRIPTION -\&Compute the electrostatical potential across the box. The potential is +\&\fB g_potential\fR computes the electrostatical potential across the box. The potential is \&calculated by first summing the charges per slice and then integrating \&twice of this charge distribution. Periodic boundaries are not taken \&into account. Reference of potential is taken to be the left side of -\&the box. It's also possible to calculate the potential in spherical +\&the box. It is also possible to calculate the potential in spherical \&coordinates as function of r by calculating a charge distribution in \&spherical slices and twice integrating them. epsilon_r is taken as 1, -\&2 is more appropriate in many cases. +\&but 2 is more appropriate in many cases. .SH FILES .BI "\-f" " traj.xtc" .B Input @@ -81,7 +81,7 @@ g_potential - calculates the electrostatic potential across the box Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_principal.1 b/man/man1/g_principal.1 index eb19599f00..08ff893b48 100644 --- a/man/man1/g_principal.1 +++ b/man/man1/g_principal.1 @@ -1,8 +1,8 @@ -.TH g_principal 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_principal - calculates axes of inertia for a group of atoms -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_principal\fP .BI "\-f" " traj.xtc " @@ -22,7 +22,7 @@ g_principal - calculates axes of inertia for a group of atoms .BI "\-[no]w" "" .BI "\-[no]foo" "" .SH DESCRIPTION -\&g_principal calculates the three principal axes of inertia for a group +\&\fB g_principal\fR calculates the three principal axes of inertia for a group \&of atoms. .SH FILES .BI "\-f" " traj.xtc" @@ -76,7 +76,7 @@ g_principal - calculates axes of inertia for a group of atoms Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]foo" "no " Dummy option to avoid empty array diff --git a/man/man1/g_protonate.1 b/man/man1/g_protonate.1 index 5f8d79d76f..6ee442111a 100644 --- a/man/man1/g_protonate.1 +++ b/man/man1/g_protonate.1 @@ -1,8 +1,8 @@ -.TH g_protonate 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_protonate - protonates structures -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_protonate\fP .BI "\-s" " topol.tpr " @@ -16,15 +16,15 @@ g_protonate - protonates structures .BI "\-e" " time " .BI "\-dt" " time " .SH DESCRIPTION -\&\fB protonate\fR reads (a) conformation(s) and adds all missing -\&hydrogens as defined in \fB ffgmx2.hdb\fR. If only \fB \-s\fR is +\&\fB g_protonate\fR reads (a) conformation(s) and adds all missing +\&hydrogens as defined in \fB gmx2.ff/aminoacids.hdb\fR. If only \fB \-s\fR is \&specified, this conformation will be protonated, if also \fB \-f\fR -\&is specified, the conformation(s) will be read from this file +\&is specified, the conformation(s) will be read from this file, \&which can be either a single conformation or a trajectory. \& -\&If a pdb file is supplied, residue names might not correspond to +\&If a \fB .pdb\fR file is supplied, residue names might not correspond to \&to the GROMACS naming conventions, in which case these residues will \&probably not be properly protonated. \& diff --git a/man/man1/g_rama.1 b/man/man1/g_rama.1 index 4cc33adee3..a391744237 100644 --- a/man/man1/g_rama.1 +++ b/man/man1/g_rama.1 @@ -1,8 +1,8 @@ -.TH g_rama 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rama - computes Ramachandran plots -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rama\fP .BI "\-f" " traj.xtc " @@ -17,7 +17,7 @@ g_rama - computes Ramachandran plots .BI "\-[no]w" "" .BI "\-xvg" " enum " .SH DESCRIPTION -\&g_rama selects the Phi/Psi dihedral combinations from your topology file +\&\fB g_rama\fR selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file \&and computes these as a function of time. \&Using simple Unix tools such as \fI grep\fR you can select out \&specific residues. @@ -54,7 +54,7 @@ g_rama - computes Ramachandran plots Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_rdf.1 b/man/man1/g_rdf.1 index 9e15a5c28e..2bc97b99e6 100644 --- a/man/man1/g_rdf.1 +++ b/man/man1/g_rdf.1 @@ -1,8 +1,8 @@ -.TH g_rdf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rdf - calculates radial distribution functions -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rdf\fP .BI "\-f" " traj.xtc " @@ -42,22 +42,22 @@ g_rdf - calculates radial distribution functions \&a scattering experiment. -\&g_rdf calculates radial distribution functions in different ways. +\&\fB g_rdf\fR calculates radial distribution functions in different ways. \&The normal method is around a (set of) particle(s), the other methods \&are around the center of mass of a set of particles (\fB \-com\fR) \&or to the closest particle in a set (\fB \-surf\fR). -\&With all methods rdf's can also be calculated around axes parallel -\&to the z\-axis with option \fB \-xy\fR. +\&With all methods, the RDF can also be calculated around axes parallel +\&to the \fI z\fR\-axis with option \fB \-xy\fR. \&With option \fB \-surf\fR normalization can not be used. -\&The option \fB \-rdf\fR sets the type of rdf to be computed. +\&The option \fB \-rdf\fR sets the type of RDF to be computed. \&Default is for atoms or particles, but one can also select center -\&of mass or geometry of molecules or residues. In all cases only +\&of mass or geometry of molecules or residues. In all cases, only \&the atoms in the index groups are taken into account. -\&For molecules and/or the center of mass option a run input file +\&For molecules and/or the center of mass option, a run input file \&is required. -\&Other weighting than COM or COG can currently only be achieved +\&Weighting other than COM or COG can currently only be achieved \&by providing a run input file with different masses. \&Options \fB \-com\fR and \fB \-surf\fR also work in conjunction \&with \fB \-rdf\fR. @@ -65,17 +65,17 @@ g_rdf - calculates radial distribution functions \&If a run input file is supplied (\fB \-s\fR) and \fB \-rdf\fR is set \&to \fB atom\fR, exclusions defined -\&in that file are taken into account when calculating the rdf. +\&in that file are taken into account when calculating the RDF. \&The option \fB \-cut\fR is meant as an alternative way to avoid -\&intramolecular peaks in the rdf plot. +\&intramolecular peaks in the RDF plot. \&It is however better to supply a run input file with a higher number of -\&exclusions. For eg. benzene a topology with nrexcl set to 5 -\&would eliminate all intramolecular contributions to the rdf. +\&exclusions. For e.g. benzene a topology, setting nrexcl to 5 +\&would eliminate all intramolecular contributions to the RDF. \&Note that all atoms in the selected groups are used, also the ones \&that don't have Lennard\-Jones interactions. -\&Option \fB \-cn\fR produces the cumulative number rdf, +\&Option \fB \-cn\fR produces the cumulative number RDF, \&i.e. the average number of particles within a distance r. @@ -135,7 +135,7 @@ g_rdf - calculates radial distribution functions Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_rms.1 b/man/man1/g_rms.1 index 1cb58ec89f..5cdb82af91 100644 --- a/man/man1/g_rms.1 +++ b/man/man1/g_rms.1 @@ -1,8 +1,8 @@ -.TH g_rms 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rms - calculates rmsd's with a reference structure and rmsd matrices -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rms\fP .BI "\-s" " topol.tpr " @@ -40,10 +40,10 @@ g_rms - calculates rmsd's with a reference structure and rmsd matrices .BI "\-nlevels" " int " .BI "\-ng" " int " .SH DESCRIPTION -\&g_rms compares two structures by computing the root mean square -\&deviation (RMSD), the size\-independent 'rho' similarity parameter -\&(rho) or the scaled rho (rhosc), -\&see Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995). +\&\fB g_rms\fR compares two structures by computing the root mean square +\&deviation (RMSD), the size\-independent [GRK]rho[grk] similarity parameter +\&(\fB rho\fR) or the scaled [GRK]rho[grk] (\fB rhosc\fR), +\&see Maiorov & Crippen, Proteins \fB 22\fR, 273 (1995). \&This is selected by \fB \-what\fR. Each structure from a trajectory (\fB \-f\fR) is compared to a @@ -54,7 +54,7 @@ Each structure from a trajectory (\fB \-f\fR) is compared to a \&With option \fB \-mir\fR also a comparison with the mirror image of \&the reference structure is calculated. \&This is useful as a reference for 'significant' values, see -\&Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995). +\&Maiorov & Crippen, Proteins \fB 22\fR, 273 (1995). \&Option \fB \-prev\fR produces the comparison with a previous frame @@ -74,10 +74,10 @@ Each structure from a trajectory (\fB \-f\fR) is compared to a \&Option \fB \-mw\fR controls whether mass weighting is done or not. \&If you select the option (default) and -\&supply a valid tpr file masses will be taken from there, -\&otherwise the masses will be deduced from the atommass.dat file in -\&the GROMACS library directory. This is fine for proteins but not -\&necessarily for other molecules. A default mass of 12.011 amu (Carbon) +\&supply a valid \fB .tpr\fR file masses will be taken from there, +\&otherwise the masses will be deduced from the \fB atommass.dat\fR file in +\&\fB GMXLIB\fR. This is fine for proteins, but not +\&necessarily for other molecules. A default mass of 12.011 amu (carbon) \&is assigned to unknown atoms. You can check whether this happend by \&turning on the \fB \-debug\fR flag and inspecting the log file. @@ -161,7 +161,7 @@ Each structure from a trajectory (\fB \-f\fR) is compared to a Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_rmsdist.1 b/man/man1/g_rmsdist.1 index 07721cc6eb..21fe01f490 100644 --- a/man/man1/g_rmsdist.1 +++ b/man/man1/g_rmsdist.1 @@ -1,8 +1,8 @@ -.TH g_rmsdist 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty" +.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6 -.B VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rmsdist\fP .BI "\-f" " traj.xtc " @@ -29,16 +29,16 @@ g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6 .BI "\-[no]sumh" "" .BI "\-[no]pbc" "" .SH DESCRIPTION -\&g_rmsdist computes the root mean square deviation of atom distances, +\&\fB g_rmsdist\fR computes the root mean square deviation of atom distances, \&which has the advantage that no fit is needed like in standard RMS -\&deviation as computed by g_rms. +\&deviation as computed by \fB g_rms\fR. \&The reference structure is taken from the structure file. -\&The rmsd at time t is calculated as the rms +\&The RMSD at time t is calculated as the RMS \&of the differences in distance between atom\-pairs in the reference \&structure and the structure at time t. -\&g_rmsdist can also produce matrices of the rms distances, rms distances +\&\fB g_rmsdist\fR can also produce matrices of the rms distances, rms distances \&scaled with the mean distance and the mean distances and matrices with \&NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists \&of atom pairs with 1/r3 and 1/r6 averaged distance below the @@ -120,7 +120,7 @@ g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6 Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_rmsf.1 b/man/man1/g_rmsf.1 index d29a510d22..88687c5695 100644 --- a/man/man1/g_rmsf.1 +++ b/man/man1/g_rmsf.1 @@ -1,8 +1,8 @@ -.TH g_rmsf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rmsf - calculates atomic fluctuations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rmsf\fP .BI "\-f" " traj.xtc " @@ -27,14 +27,14 @@ g_rmsf - calculates atomic fluctuations .BI "\-[no]aniso" "" .BI "\-[no]fit" "" .SH DESCRIPTION -\&g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard -\&deviation) of atomic positions -\&after (optionally) fitting to a reference frame. +\&\fB g_rmsf\fR computes the root mean square fluctuation (RMSF, i.e. standard +\&deviation) of atomic positions in the trajectory (supplied with \fB \-f\fR) +\&after (optionally) fitting to a reference frame (supplied with \fB \-s\fR). \&With option \fB \-oq\fR the RMSF values are converted to B\-factor -\&values, which are written to a pdb file with the coordinates, of the -\&structure file, or of a pdb file when \fB \-q\fR is specified. +\&values, which are written to a \fB .pdb\fR file with the coordinates, of the +\&structure file, or of a \fB .pdb\fR file when \fB \-q\fR is specified. \&Option \fB \-ox\fR writes the B\-factors to a file with the average \&coordinates. @@ -43,18 +43,18 @@ g_rmsf - calculates atomic fluctuations \&respect to the reference structure is calculated. -\&With the option \fB aniso\fR g_rmsf will compute anisotropic +\&With the option \fB \-aniso\fR, \fB g_rmsf\fR will compute anisotropic \&temperature factors and then it will also output average coordinates -\&and a pdb file with ANISOU records (corresonding to the \fB \-oq\fR +\&and a \fB .pdb\fR file with ANISOU records (corresonding to the \fB \-oq\fR \&or \fB \-ox\fR option). Please note that the U values -\&are orientation dependent, so before comparison with experimental data +\&are orientation\-dependent, so before comparison with experimental data \&you should verify that you fit to the experimental coordinates. -\&When a pdb input file is passed to the program and the \fB \-aniso\fR +\&When a \fB .pdb\fR input file is passed to the program and the \fB \-aniso\fR \&flag is set \&a correlation plot of the Uij will be created, if any anisotropic -\&temperature factors are present in the pdb file. +\&temperature factors are present in the \fB .pdb\fR file. \&With option \fB \-dir\fR the average MSF (3x3) matrix is diagonalized. @@ -121,7 +121,7 @@ g_rmsf - calculates atomic fluctuations Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_rotacf.1 b/man/man1/g_rotacf.1 index 3a42027a2f..84e6d6fb6b 100644 --- a/man/man1/g_rotacf.1 +++ b/man/man1/g_rotacf.1 @@ -1,8 +1,8 @@ -.TH g_rotacf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rotacf - calculates the rotational correlation function for molecules -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rotacf\fP .BI "\-f" " traj.xtc " @@ -27,13 +27,13 @@ g_rotacf - calculates the rotational correlation function for molecules .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_rotacf calculates the rotational correlation function +\&\fB g_rotacf\fR calculates the rotational correlation function \&for molecules. Three atoms (i,j,k) must be given in the index -\&file, defining two vectors ij and jk. The rotational acf +\&file, defining two vectors ij and jk. The rotational ACF \&is calculated as the autocorrelation function of the vector \&n = ij x jk, i.e. the cross product of the two vectors. \&Since three atoms span a plane, the order of the three atoms -\&does not matter. Optionally, controlled by the \-d switch, you can +\&does not matter. Optionally, controlled by the \fB \-d\fR switch, you can \&calculate the rotational correlation function for linear molecules \&by specifying two atoms (i,j) in the index file. \& @@ -42,15 +42,14 @@ g_rotacf - calculates the rotational correlation function for molecules \&EXAMPLES -\&g_rotacf \-P 1 \-nparm 2 \-fft \-n index \-o rotacf\-x\-P1 -\&\-fa expfit\-x\-P1 \-beginfit 2.5 \-endfit 20.0 +\&\fB g_rotacf \-P 1 \-nparm 2 \-fft \-n index \-o rotacf\-x\-P1 +\&\-fa expfit\-x\-P1 \-beginfit 2.5 \-endfit 20.0\fR \&This will calculate the rotational correlation function using a first \&order Legendre polynomial of the angle of a vector defined by the index -\&file. The correlation function will be fitted from 2.5 ps till 20.0 ps -\&to a two parameter exponential. -\& +\&file. The correlation function will be fitted from 2.5 ps until 20.0 ps +\&to a two\-parameter exponential. .SH FILES .BI "\-f" " traj.xtc" .B Input @@ -88,7 +87,7 @@ g_rotacf - calculates the rotational correlation function for molecules Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -109,7 +108,7 @@ g_rotacf - calculates the rotational correlation function for molecules Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_rotmat.1 b/man/man1/g_rotmat.1 index cf26c4fb95..b4b836fb99 100644 --- a/man/man1/g_rotmat.1 +++ b/man/man1/g_rotmat.1 @@ -1,8 +1,8 @@ -.TH g_rotmat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty" +.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_rotmat - plots the rotation matrix for fitting to a reference structure -.B VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_rotmat\fP .BI "\-f" " traj.xtc " @@ -22,7 +22,7 @@ g_rotmat - plots the rotation matrix for fitting to a reference structure .BI "\-[no]fitxy" "" .BI "\-[no]mw" "" .SH DESCRIPTION -\&g_rotmat plots the rotation matrix required for least squares fitting +\&\fB g_rotmat\fR plots the rotation matrix required for least squares fitting \&a conformation onto the reference conformation provided with \&\fB \-s\fR. Translation is removed before fitting. \&The output are the three vectors that give the new directions @@ -36,7 +36,7 @@ g_rotmat - plots the rotation matrix for fitting to a reference structure \&determining the orientation of a molecule \&at an interface, possibly on a trajectory produced with \&\fB trjconv \-fit rotxy+transxy\fR to remove the rotation -\&in the xy\-plane. +\&in the \fI x\-y\fR plane. \& @@ -45,12 +45,12 @@ g_rotmat - plots the rotation matrix for fitting to a reference structure \&the lowest sum of RMSD's to all other structures is used. \&Since the computational cost of this procedure grows with \&the square of the number of frames, the \fB \-skip\fR option -\&can be useful. A full fit or only a fit in the x/y plane can +\&can be useful. A full fit or only a fit in the \fI x\-y\fR plane can \&be performed. \& -\&Option \fB \-fitxy\fR fits in the x/y plane before determining +\&Option \fB \-fitxy\fR fits in the \fI x\-y\fR plane before determining \&the rotation matrix. .SH FILES .BI "\-f" " traj.xtc" @@ -89,7 +89,7 @@ g_rotmat - plots the rotation matrix for fitting to a reference structure Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -98,7 +98,7 @@ g_rotmat - plots the rotation matrix for fitting to a reference structure Determine the optimal reference structure: \fB none\fR, \fB xyz\fR or \fB xy\fR .BI "\-skip" " int" " 1" - Use every nr\-th frame for \-ref + Use every nr\-th frame for \fB \-ref\fR .BI "\-[no]fitxy" "no " Fit the x/y rotation before determining the rotation diff --git a/man/man1/g_saltbr.1 b/man/man1/g_saltbr.1 index 7b845e4aa9..197fdf528f 100644 --- a/man/man1/g_saltbr.1 +++ b/man/man1/g_saltbr.1 @@ -1,8 +1,8 @@ -.TH g_saltbr 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_saltbr - computes salt bridges -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_saltbr\fP .BI "\-f" " traj.xtc " @@ -16,15 +16,16 @@ g_saltbr - computes salt bridges .BI "\-t" " real " .BI "\-[no]sep" "" .SH DESCRIPTION -\&g_saltbr plots the distance between all combination of charged groups +\&\fB g_saltbr\fR plots the distance between all combination of charged groups \&as a function of time. The groups are combined in different ways. -\&A minimum distance can be given, (eg. the cut\-off), then groups +\&A minimum distance can be given (i.e. a cut\-off), such that groups \&that are never closer than that distance will not be plotted. -\&Output will be in a number of fixed filenames, min\-min.xvg, plus\-min.xvg -\&and plus\-plus.xvg, or files for every individual ion\-pair if the \fB \-sep\fR -\&option is selected. In this case files are named as \fB sb\-ResnameResnr\-Atomnr\fR. -\&There may be many such files. + +\&Output will be in a number of fixed filenames, \fB min\-min.xvg\fR, \fB plus\-min.xvg\fR +\&and \fB plus\-plus.xvg\fR, or files for every individual ion pair if the \fB \-sep\fR +\&option is selected. In this case, files are named as \fB sb\-(Resname)(Resnr)\-(Atomnr)\fR. +\&There may be \fB many\fR such files. .SH FILES .BI "\-f" " traj.xtc" .B Input diff --git a/man/man1/g_sas.1 b/man/man1/g_sas.1 index abfca19da7..657a7f61f0 100644 --- a/man/man1/g_sas.1 +++ b/man/man1/g_sas.1 @@ -1,8 +1,8 @@ -.TH g_sas 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_sas - computes solvent accessible surface area -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_sas\fP .BI "\-f" " traj.xtc " @@ -31,17 +31,17 @@ g_sas - computes solvent accessible surface area .BI "\-[no]prot" "" .BI "\-dgs" " real " .SH DESCRIPTION -\&g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. -\&As a side effect the Connolly surface can be generated as well in -\&a pdb file where the nodes are represented as atoms and the vertices +\&\fB g_sas\fR computes hydrophobic, hydrophilic and total solvent accessible surface area. +\&As a side effect, the Connolly surface can be generated as well in +\&a \fB .pdb\fR file where the nodes are represented as atoms and the vertices \&connecting the nearest nodes as CONECT records. \&The program will ask for a group for the surface calculation \&and a group for the output. The calculation group should always \&consists of all the non\-solvent atoms in the system. \&The output group can be the whole or part of the calculation group. -\&The area can be plotted +\&The average and standard deviation of the area over the trajectory can be plotted \&per residue and atom as well (options \fB \-or\fR and \fB \-oa\fR). -\&In combination with the latter option an \fB itp\fR file can be +\&In combination with the latter option an \fB .itp\fR file can be \&generated (option \fB \-i\fR) \&which can be used to restrain surface atoms. @@ -55,9 +55,9 @@ g_sas - computes solvent accessible surface area \&Please consider whether the normal probe radius is appropriate \&in this case or whether you would rather use e.g. 0. It is good \&to keep in mind that the results for volume and density are very -\&approximate, in e.g. ice Ih one can easily fit water molecules in the -\&pores which would yield too low volume, too high surface area and too -\&high density. +\&approximate. For example, in ice Ih, one can easily fit water molecules in the +\&pores which would yield a volume that is too low, and surface area and density +\&that are both too high. .SH FILES .BI "\-f" " traj.xtc" .B Input @@ -115,7 +115,7 @@ g_sas - computes solvent accessible surface area Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -139,10 +139,10 @@ g_sas - computes solvent accessible surface area Take periodicity into account .BI "\-[no]prot" "yes " - Output the protein to the connelly pdb file too + Output the protein to the Connelly \fB .pdb\fR file too .BI "\-dgs" " real" " 0 " - default value for solvation free energy per area (kJ/mol/nm2) + Default value for solvation free energy per area (kJ/mol/nm2) .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_select.1 b/man/man1/g_select.1 index ed8ce52f51..f94073003d 100644 --- a/man/man1/g_select.1 +++ b/man/man1/g_select.1 @@ -1,8 +1,8 @@ -.TH g_select 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_select - selects groups of atoms based on flexible textual selections -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_select\fP .BI "\-f" " traj.xtc " @@ -31,7 +31,7 @@ g_select - selects groups of atoms based on flexible textual selections .BI "\-[no]cfnorm" "" .BI "\-resnr" " enum " .SH DESCRIPTION -\&g_select writes out basic data about dynamic selections. +\&\fB g_select\fR writes out basic data about dynamic selections. \&It can be used for some simple analyses, or the output can \&be combined with output from other programs and/or external \&analysis programs to calculate more complex things. @@ -66,7 +66,7 @@ g_select - selects groups of atoms based on flexible textual selections \&With \fB \-on\fR, the selected atoms are written as a index file -\&compatible with make_ndx and the analyzing tools. Each selection +\&compatible with \fB make_ndx\fR and the analyzing tools. Each selection \&is written as a selection group and for dynamic selections a \&group is written for each frame. diff --git a/man/man1/g_sgangle.1 b/man/man1/g_sgangle.1 index c7d48d29be..251efc0603 100644 --- a/man/man1/g_sgangle.1 +++ b/man/man1/g_sgangle.1 @@ -1,8 +1,8 @@ -.TH g_sgangle 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_sgangle - computes the angle and distance between two groups -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_sgangle\fP .BI "\-f" " traj.xtc " @@ -26,10 +26,10 @@ g_sgangle - computes the angle and distance between two groups \&Compute the angle and distance between two groups. \&The groups are defined by a number of atoms given in an index file and \&may be two or three atoms in size. -\&If \-one is set, only one group should be specified in the index +\&If \fB \-one\fR is set, only one group should be specified in the index \&file and the angle between this group at time 0 and t will be computed. \&The angles calculated depend on the order in which the atoms are -\&given. Giving for instance 5 6 will rotate the vector 5\-6 with +\&given. Giving, for instance, 5 6 will rotate the vector 5\-6 with \&180 degrees compared to giving 6 5. If three atoms are given, @@ -41,13 +41,13 @@ If three atoms are given, \&Here is what some of the file options do: -\&\-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used. +\&\fB \-oa\fR: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used. -\&\-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group. +\&\fB \-od\fR: Distance between two groups. Distance is taken from the center of one group to the center of the other group. -\&\-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately. +\&\fB \-od1\fR: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately. -\&\-od2: For two planes this option has no meaning. +\&\fB \-od2\fR: For two planes this option has no meaning. .SH FILES .BI "\-f" " traj.xtc" .B Input @@ -97,7 +97,7 @@ If three atoms are given, Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -106,7 +106,7 @@ If three atoms are given, Only one group compute angle between vector at time zero and time t .BI "\-[no]z" "no " - Use the Z\-axis as reference + Use the \fI z\fR\-axis as reference .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_sham.1 b/man/man1/g_sham.1 index 30d01a1658..03b81292de 100644 --- a/man/man1/g_sham.1 +++ b/man/man1/g_sham.1 @@ -1,8 +1,8 @@ -.TH g_sham 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_sham - read/write xmgr and xvgr data sets -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_sham\fP .BI "\-f" " graph.xvg " @@ -45,19 +45,19 @@ g_sham - read/write xmgr and xvgr data sets .BI "\-nlevels" " int " .BI "\-mname" " string " .SH DESCRIPTION -\&g_sham makes multi\-dimensional free\-energy, enthalpy and entropy plots. -\&g_sham reads one or more xvg files and analyzes data sets. -\&g_sham basic purpose is plotting Gibbs free energy landscapes +\&\fB g_sham\fR makes multi\-dimensional free\-energy, enthalpy and entropy plots. +\&\fB g_sham\fR reads one or more \fB .xvg\fR files and analyzes data sets. +\&The basic purpose of \fB g_sham\fR is to plot Gibbs free energy landscapes \&(option \fB \-ls\fR) -\&by Bolzmann inverting multi\-dimensional histograms (option \fB \-lp\fR) +\&by Bolzmann inverting multi\-dimensional histograms (option \fB \-lp\fR), \&but it can also \&make enthalpy (option \fB \-lsh\fR) and entropy (option \fB \-lss\fR) \&plots. The histograms can be made for any quantities the user supplies. \&A line in the input file may start with a time -\&(see option \fB \-time\fR) and any number of y values may follow. +\&(see option \fB \-time\fR) and any number of \fI y\fR\-values may follow. \&Multiple sets can also be \&read when they are separated by & (option \fB \-n\fR), -\&in this case only one y value is read from each line. +\&in this case only one \fI y\fR\-value is read from each line. \&All lines starting with and @ are skipped. \& @@ -71,23 +71,23 @@ g_sham - read/write xmgr and xvgr data sets \&Option \fB \-ene\fR can be used to supply a file with energies. \&These energies are used as a weighting function in the single -\&histogram analysis method due to Kumar et. al. When also temperatures -\&are supplied (as a second column in the file) an experimental +\&histogram analysis method by Kumar et al. When temperatures +\&are supplied (as a second column in the file), an experimental \&weighting scheme is applied. In addition the vales \&are used for making enthalpy and entropy plots. \& -\&With option \fB \-dim\fR dimensions can be gives for distances. +\&With option \fB \-dim\fR, dimensions can be gives for distances. \&When a distance is 2\- or 3\-dimensional, the circumference or surface \&sampled by two particles increases with increasing distance. \&Depending on what one would like to show, one can choose to correct \&the histogram and free\-energy for this volume effect. -\&The probability is normalized by r and r2 for a dimension of 2 and 3 +\&The probability is normalized by r and r2 for dimensions of 2 and 3, \&respectively. \&A value of \-1 is used to indicate an angle in degrees between two \&vectors: a sin(angle) normalization will be applied. -\&Note that for angles between vectors the inner\-product or cosine +\&\fB Note\fR that for angles between vectors the inner\-product or cosine \&is the natural quantity to use, as it will produce bins of the same \&volume. .SH FILES @@ -158,7 +158,7 @@ g_sham - read/write xmgr and xvgr data sets Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_sigeps.1 b/man/man1/g_sigeps.1 index 24bf17d528..868479e92e 100644 --- a/man/man1/g_sigeps.1 +++ b/man/man1/g_sigeps.1 @@ -1,8 +1,8 @@ -.TH g_sigeps 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_sigeps\fP .BI "\-o" " potje.xvg " @@ -23,10 +23,10 @@ g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon .BI "\-qj" " real " .BI "\-sigfac" " real " .SH DESCRIPTION -\&Sigeps is a simple utility that converts c6/c12 or c6/cn combinations -\&to sigma and epsilon, or vice versa. It can also plot the potential -\&in file. In addition it makes an approximation of a Buckingham potential -\&to a Lennard Jones potential. +\&\fB g_sigeps\fR is a simple utility that converts C6/C12 or C6/Cn combinations +\&to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential +\&in file. In addition, it makes an approximation of a Buckingham potential +\&to a Lennard\-Jones potential. .SH FILES .BI "\-o" " potje.xvg" .B Output @@ -43,7 +43,7 @@ g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_sorient.1 b/man/man1/g_sorient.1 index 9289f26bd5..42b95d4123 100644 --- a/man/man1/g_sorient.1 +++ b/man/man1/g_sorient.1 @@ -1,8 +1,8 @@ -.TH g_sorient 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_sorient - analyzes solvent orientation around solutes -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_sorient\fP .BI "\-f" " traj.xtc " @@ -29,17 +29,19 @@ g_sorient - analyzes solvent orientation around solutes .BI "\-rbin" " real " .BI "\-[no]pbc" "" .SH DESCRIPTION -\&g_sorient analyzes solvent orientation around solutes. +\&\fB g_sorient\fR analyzes solvent orientation around solutes. \&It calculates two angles between the vector from one or more \&reference positions to the first atom of each solvent molecule: -\&theta1: the angle with the vector from the first atom of the solvent + +\&[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent \&molecule to the midpoint between atoms 2 and 3. -\&theta2: the angle with the normal of the solvent plane, defined by the -\&same three atoms, or when the option \fB \-v23\fR is set +\&[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the +\&same three atoms, or, when the option \fB \-v23\fR is set, \&the angle with the vector between atoms 2 and 3. + \&The reference can be a set of atoms or \&the center of mass of a set of atoms. The group of solvent atoms should \&consist of 3 atoms per solvent molecule. @@ -47,18 +49,18 @@ g_sorient - analyzes solvent orientation around solutes \&considered for \fB \-o\fR and \fB \-no\fR each frame. -\&\fB \-o\fR: distribtion of cos(theta1) for rmin=r=rmax. +\&\fB \-o\fR: distribtion of cos([GRK]theta[grk]1) for rmin=r=rmax. -\&\fB \-no\fR: distribution of cos(theta2) for rmin=r=rmax. +\&\fB \-no\fR: distribution of cos([GRK]theta[grk]2) for rmin=r=rmax. -\&\fB \-ro\fR: cos(theta1) and 3cos2(theta2)\-1 as a function of the +\&\fB \-ro\fR: cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of the \&distance. \&\fB \-co\fR: the sum over all solvent molecules within distance r -\&of cos(theta1) and 3cos2(theta2)\-1 as a function of r. +\&of cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of r. \&\fB \-rc\fR: the distribution of the solvent molecules as a function of r @@ -115,7 +117,7 @@ g_sorient - analyzes solvent orientation around solutes Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_spatial.1 b/man/man1/g_spatial.1 index cab6fbcb08..fae821ba17 100644 --- a/man/man1/g_spatial.1 +++ b/man/man1/g_spatial.1 @@ -1,8 +1,8 @@ -.TH g_spatial 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_spatial 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME -g_spatial - calculates the spatial distribution function (more control than g_sdf) +g_spatial - calculates the spatial distribution function -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_spatial\fP .BI "\-s" " topol.tpr " @@ -21,57 +21,57 @@ g_spatial - calculates the spatial distribution function (more control than g_sd .BI "\-bin" " real " .BI "\-nab" " int " .SH DESCRIPTION -\&g_spatial calculates the spatial distribution function and +\&\fB g_spatial\fR calculates the spatial distribution function and \&outputs it in a form that can be read by VMD as Gaussian98 cube format. -\&This was developed from template.c (gromacs\-3.3). -\&For a system of 32K atoms and a 50ns trajectory, the SDF can be generated +\&This was developed from template.c (GROMACS\-3.3). +\&For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated \&in about 30 minutes, with most of the time dedicated to the two runs through -\&trjconv that are required to center everything properly. -\&This also takes a whole bunch of space (3 copies of the xtc file). +\&\fB trjconv\fR that are required to center everything properly. +\&This also takes a whole bunch of space (3 copies of the \fB .xtc\fR file). \&Still, the pictures are pretty and very informative when the fitted selection is properly made. -\&3\-4 atoms in a widely mobile group like a free amino acid in solution works +\&3\-4 atoms in a widely mobile group (like a free amino acid in solution) works \&well, or select the protein backbone in a stable folded structure to get the SDF \&of solvent and look at the time\-averaged solvation shell. -\&It is also possible using this program to generate the SDF based on some arbitrarty -\&Cartesian coordinate. To do that, simply omit the preliminary trjconv steps. +\&It is also possible using this program to generate the SDF based on some arbitrary +\&Cartesian coordinate. To do that, simply omit the preliminary \fB trjconv\fR steps. \&USAGE: -\&1. Use make_ndx to create a group containing the atoms around which you want the SDF +\&1. Use \fB make_ndx\fR to create a group containing the atoms around which you want the SDF -\&2. trjconv \-s a.tpr \-f a.xtc \-o b.xtc \-center tric \-ur compact \-pbc none +\&2. \fB trjconv \-s a.tpr \-f a.xtc \-o b.xtc \-center tric \-ur compact \-pbc none\fR -\&3. trjconv \-s a.tpr \-f b.xtc \-o c.xtc \-fit rot+trans +\&3. \fB trjconv \-s a.tpr \-f b.xtc \-o c.xtc \-fit rot+trans\fR -\&4. run g_spatial on the xtc output of step 3. +\&4. run \fB g_spatial\fR on the \fB .xtc\fR output of step 3. -\&5. Load grid.cube into VMD and view as an isosurface. +\&5. Load \fB grid.cube\fR into VMD and view as an isosurface. -\&*** Systems such as micelles will require trjconv \-pbc cluster between steps 1 and 2 +\&\fB Note\fR that systems such as micelles will require \fB trjconv \-pbc cluster\fR between steps 1 and 2 -\&WARNINGS: +\&WARNINGS: \&The SDF will be generated for a cube that contains all bins that have some non\-zero occupancy. -\&However, the preparatory \-fit rot+trans option to trjconv implies that your system will be rotating +\&However, the preparatory \fB \-fit rot+trans\fR option to \fB trjconv\fR implies that your system will be rotating \&and translating in space (in order that the selected group does not). Therefore the values that are \&returned will only be valid for some region around your central group/coordinate that has full overlap \&with system volume throughout the entire translated/rotated system over the course of the trajectory. \&It is up to the user to ensure that this is the case. -\&BUGS: +\&BUGS: \&When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected -\&and the program is halted prior to the fault while displaying a warning message suggesting the use of the \-nab +\&and the program is halted prior to the fault while displaying a warning message suggesting the use of the \fB \-nab\fR (Number of Additional Bins) \&option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again -\&with an increased \-nab value. +\&with an increased \fB \-nab\fR value. -\&RISKY OPTIONS: +\&RISKY OPTIONS: \&To reduce the amount of space and time required, you can output only the coords -\&that are going to be used in the first and subsequent run through trjconv. -\&However, be sure to set the \-nab option to a sufficiently high value since -\&memory is allocated for cube bins based on the initial coords and the \-nab -\&(Number of Additional Bins) option value. +\&that are going to be used in the first and subsequent run through \fB trjconv\fR. +\&However, be sure to set the \fB \-nab\fR option to a sufficiently high value since +\&memory is allocated for cube bins based on the initial coordinates and the \fB \-nab\fR +\&option value. .SH FILES .BI "\-s" " topol.tpr" @@ -106,13 +106,13 @@ g_spatial - calculates the spatial distribution function (more control than g_sd Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]pbc" "no " Use periodic boundary conditions for computing distances .BI "\-[no]div" "yes " - Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (\-nodiv) to get accurate counts per frame + Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (\fB \-nodiv\fR) to get accurate counts per frame .BI "\-ign" " int" " \-1" Do not display this number of outer cubes (positive values may reduce boundary speckles; \-1 ensures outer surface is visible) diff --git a/man/man1/g_spol.1 b/man/man1/g_spol.1 index 9670024156..e5d24c82ad 100644 --- a/man/man1/g_spol.1 +++ b/man/man1/g_spol.1 @@ -1,8 +1,8 @@ -.TH g_spol 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_spol - analyzes solvent dipole orientation and polarization around solutes -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_spol\fP .BI "\-f" " traj.xtc " @@ -24,7 +24,7 @@ g_spol - analyzes solvent dipole orientation and polarization around solutes .BI "\-dip" " real " .BI "\-bw" " real " .SH DESCRIPTION -\&g_spol analyzes dipoles around a solute; it is especially useful +\&\fB g_spol\fR analyzes dipoles around a solute; it is especially useful \&for polarizable water. A group of reference atoms, or a center \&of mass reference (option \fB \-com\fR) and a group of solvent \&atoms is required. The program splits the group of solvent atoms @@ -35,7 +35,7 @@ g_spol - analyzes solvent dipole orientation and polarization around solutes \&the inner product of the distance vector \&and the dipole of the solvent molecule is determined. \&For solvent molecules with net charge (ions), the net charge of the ion -\&is subtracted evenly at all atoms in the selection of each ion. +\&is subtracted evenly from all atoms in the selection of each ion. \&The average of these dipole components is printed. \&The same is done for the polarization, where the average dipole is \&subtracted from the instantaneous dipole. The magnitude of the average @@ -79,7 +79,7 @@ g_spol - analyzes solvent dipole orientation and polarization around solutes Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR diff --git a/man/man1/g_tcaf.1 b/man/man1/g_tcaf.1 index 84bb83f542..f9d48b1e9a 100644 --- a/man/man1/g_tcaf.1 +++ b/man/man1/g_tcaf.1 @@ -1,8 +1,8 @@ -.TH g_tcaf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_tcaf - calculates viscosities of liquids -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_tcaf\fP .BI "\-f" " traj.trr " @@ -33,45 +33,45 @@ g_tcaf - calculates viscosities of liquids .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_tcaf computes tranverse current autocorrelations. -\&These are used to estimate the shear viscosity eta. -\&For details see: Palmer, JCP 49 (1994) pp 359\-366. +\&\fB g_tcaf\fR computes tranverse current autocorrelations. +\&These are used to estimate the shear viscosity, [GRK]eta[grk]. +\&For details see: Palmer, Phys. Rev. E 49 (1994) pp 359\-366. \&Transverse currents are calculated using the -\&k\-vectors (1,0,0) and (2,0,0) each also in the y\- and z\-direction, +\&k\-vectors (1,0,0) and (2,0,0) each also in the \fI y\fR\- and \fI z\fR\-direction, \&(1,1,0) and (1,\-1,0) each also in the 2 other planes (these vectors \&are not independent) and (1,1,1) and the 3 other box diagonals (also \¬ independent). For each k\-vector the sine and cosine are used, in \&combination with the velocity in 2 perpendicular directions. This gives \&a total of 16*2*2=64 transverse currents. One autocorrelation is -\&calculated fitted for each k\-vector, which gives 16 tcaf's. Each of -\&these tcaf's is fitted to f(t) = exp(\-v)(cosh(Wv) + 1/W sinh(Wv)), -\&v = \-t/(2 tau), W = sqrt(1 \- 4 tau eta/rho k2), which gives 16 tau's -\&and eta's. The fit weights decay with time as exp(\-t/wt), the tcaf and +\&calculated fitted for each k\-vector, which gives 16 TCAF's. Each of +\&these TCAF's is fitted to f(t) = exp(\-v)(cosh(Wv) + 1/W sinh(Wv)), +\&v = \-t/(2 [GRK]tau[grk]), W = sqrt(1 \- 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k2), which gives 16 values of [GRK]tau[grk] +\&and [GRK]eta[grk]. The fit weights decay with time as exp(\-t/wt), and the TCAF and \&fit are calculated up to time 5*wt. -\&The eta's should be fitted to 1 \- a eta(k) k2, from which +\&The [GRK]eta[grk] values should be fitted to 1 \- a [GRK]eta[grk](k) k2, from which \&one can estimate the shear viscosity at k=0. \&When the box is cubic, one can use the option \fB \-oc\fR, which -\&averages the tcaf's over all k\-vectors with the same length. +\&averages the TCAF's over all k\-vectors with the same length. \&This results in more accurate tcaf's. -\&Both the cubic tcaf's and fits are written to \fB \-oc\fR -\&The cubic eta estimates are also written to \fB \-ov\fR. +\&Both the cubic TCAF's and fits are written to \fB \-oc\fR +\&The cubic [GRK]eta[grk] estimates are also written to \fB \-ov\fR. -\&With option \fB \-mol\fR the transverse current is determined of -\&molecules instead of atoms. In this case the index group should +\&With option \fB \-mol\fR, the transverse current is determined of +\&molecules instead of atoms. In this case, the index group should \&consist of molecule numbers instead of atom numbers. \&The k\-dependent viscosities in the \fB \-ov\fR file should be -\&fitted to eta(k) = eta0 (1 \- a k2) to obtain the viscosity at +\&fitted to [GRK]eta[grk](k) = [GRK]eta[grk]0 (1 \- a k2) to obtain the viscosity at \&infinite wavelength. -\&NOTE: make sure you write coordinates and velocities often enough. +\&\fB Note:\fR make sure you write coordinates and velocities often enough. \&The initial, non\-exponential, part of the autocorrelation function \&is very important for obtaining a good fit. .SH FILES @@ -131,7 +131,7 @@ g_tcaf - calculates viscosities of liquids Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -155,7 +155,7 @@ g_tcaf - calculates viscosities of liquids Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_traj.1 b/man/man1/g_traj.1 index b1d0f999b8..1d8f8e82be 100644 --- a/man/man1/g_traj.1 +++ b/man/man1/g_traj.1 @@ -1,8 +1,8 @@ -.TH g_traj 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_traj\fP .BI "\-f" " traj.xtc " @@ -41,9 +41,10 @@ g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory .BI "\-[no]len" "" .BI "\-[no]fp" "" .BI "\-bin" " real " +.BI "\-ctime" " real " .BI "\-scale" " real " .SH DESCRIPTION -\&g_traj plots coordinates, velocities, forces and/or the box. +\&\fB g_traj\fR plots coordinates, velocities, forces and/or the box. \&With \fB \-com\fR the coordinates, velocities and forces are \&calculated for the center of mass of each group. \&When \fB \-mol\fR is set, the numbers in the index file are @@ -64,15 +65,16 @@ g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory \&Options \fB \-cv\fR and \fB \-cf\fR write the average velocities -\&and average forces as temperature factors to a pdb file with -\&the average coordinates. The temperature factors are scaled such -\&that the maximum is 10. The scaling can be changed with the option -\&\fB \-scale\fR. To get the velocities or forces of one +\&and average forces as temperature factors to a \fB .pdb\fR file with +\&the average coordinates or the coordinates at \fB \-ctime\fR. +\&The temperature factors are scaled such that the maximum is 10. +\&The scaling can be changed with the option \fB \-scale\fR. +\&To get the velocities or forces of one \&frame set both \fB \-b\fR and \fB \-e\fR to the time of \&desired frame. When averaging over frames you might need to use \&the \fB \-nojump\fR option to obtain the correct average coordinates. \&If you select either of these option the average force and velocity -\&for each atom are written to an xvg file as well +\&for each atom are written to an \fB .xvg\fR file as well \&(specified with \fB \-av\fR or \fB \-af\fR). @@ -167,7 +169,7 @@ g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -205,8 +207,11 @@ g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory .BI "\-bin" " real" " 1 " Binwidth for velocity histogram (nm/ps) +.BI "\-ctime" " real" " \-1 " + Use frame at this time for x in \fB \-cv\fR and \fB \-cf\fR instead of the average x + .BI "\-scale" " real" " 0 " - Scale factor for pdb output, 0 is autoscale + Scale factor for \fB .pdb\fR output, 0 is autoscale .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_tune_pme.1 b/man/man1/g_tune_pme.1 index 66010326cc..59c4f7264a 100644 --- a/man/man1/g_tune_pme.1 +++ b/man/man1/g_tune_pme.1 @@ -1,8 +1,8 @@ -.TH g_tune_pme 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_tune_pme 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_tune_pme - time mdrun as a function of PME nodes to optimize settings -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_tune_pme\fP .BI "\-p" " perf.out " @@ -65,6 +65,7 @@ g_tune_pme - time mdrun as a function of PME nodes to optimize settings .BI "\-max" " real " .BI "\-min" " real " .BI "\-npme" " enum " +.BI "\-fix" " int " .BI "\-upfac" " real " .BI "\-downfac" " real " .BI "\-ntpr" " int " @@ -96,12 +97,12 @@ g_tune_pme - time mdrun as a function of PME nodes to optimize settings .BI "\-[no]ionize" "" .SH DESCRIPTION \&For a given number \fB \-np\fR or \fB \-nt\fR of processors/threads, this program systematically -\× mdrun with various numbers of PME\-only nodes and determines +\× \fB mdrun\fR with various numbers of PME\-only nodes and determines \&which setting is fastest. It will also test whether performance can \&be enhanced by shifting load from the reciprocal to the real space \&part of the Ewald sum. -\&Simply pass your \fB .tpr\fR file to g_tune_pme together with other options -\&for mdrun as needed. +\&Simply pass your \fB .tpr\fR file to \fB g_tune_pme\fR together with other options +\&for \fB mdrun\fR as needed. \&Which executables are used can be set in the environment variables @@ -109,23 +110,25 @@ g_tune_pme - time mdrun as a function of PME nodes to optimize settings \&will be used as defaults. Note that for certain MPI frameworks you \&need to provide a machine\- or hostfile. This can also be passed \&via the MPIRUN variable, e.g. -\&'export MPIRUN="/usr/local/mpirun \-machinefile hosts"' -\&Please call g_tune_pme with the normal options you would pass to -\&mdrun and add \fB \-np\fR for the number of processors to perform the +\&\fB export MPIRUN="/usr/local/mpirun \-machinefile hosts"\fR + + +\&Please call \fB g_tune_pme\fR with the normal options you would pass to +\&\fB mdrun\fR and add \fB \-np\fR for the number of processors to perform the \&tests on, or \fB \-nt\fR for the number of threads. You can also add \fB \-r\fR \&to repeat each test several times to get better statistics. -\&g_tune_pme can test various real space / reciprocal space workloads +\&\fB g_tune_pme\fR can test various real space / reciprocal space workloads \&for you. With \fB \-ntpr\fR you control how many extra \fB .tpr\fR files will be \&written with enlarged cutoffs and smaller fourier grids respectively. -\&Typically, the first test (no. 0) will be with the settings from the input -\&\fB .tpr\fR file; the last test (no. \fB ntpr\fR) will have cutoffs multiplied +\&Typically, the first test (number 0) will be with the settings from the input +\&\fB .tpr\fR file; the last test (number \fB ntpr\fR) will have cutoffs multiplied \&by (and at the same time fourier grid dimensions divided by) the scaling -\&factor \fB \-fac\fR (default 1.2). The remaining \fB .tpr\fR files will have equally -\&spaced values inbetween these extremes. Note that you can set \fB \-ntpr\fR to 1 +\&factor \fB \-fac\fR (default 1.2). The remaining \fB .tpr\fR files will have about +\&equally\-spaced values in between these extremes. \fB Note\fR that you can set \fB \-ntpr\fR to 1 \&if you just want to find the optimal number of PME\-only nodes; in that case \&your input \fB .tpr\fR file will remain unchanged. @@ -136,15 +139,15 @@ g_tune_pme - time mdrun as a function of PME nodes to optimize settings \&are by default reset after 100 steps. For large systems \&(1M atoms) you may have to set \fB \-resetstep\fR to a higher value. \&From the 'DD' load imbalance entries in the md.log output file you -\&can tell after how many steps the load is sufficiently balanced. +\&can tell after how many steps the load is sufficiently balanced. Example call: -Example call: \fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR +\fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR -\&After calling mdrun several times, detailed performance information -\&is available in the output file perf.out. -\&Note that during the benchmarks a couple of temporary files are written -\&(options \-b*), these will be automatically deleted after each test. +\&After calling \fB mdrun\fR several times, detailed performance information +\&is available in the output file \fB perf.out.\fR +\&\fB Note\fR that during the benchmarks, a couple of temporary files are written +\&(options \fB \-b\fR*), these will be automatically deleted after each test. \&If you want the simulation to be started automatically with the @@ -365,7 +368,7 @@ Example call: \fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR Number of nodes to run the tests on (must be 2 for separate PME nodes) .BI "\-npstring" " enum" " \-np" - Specify the number of processors to $MPIRUN using this string: \fB \-np\fR, \fB \-n\fR or \fB none\fR + Specify the number of processors to \fB $MPIRUN\fR using this string: \fB \-np\fR, \fB \-n\fR or \fB none\fR .BI "\-nt" " int" " 1" Number of threads to run the tests on (turns MPI & mpirun off) @@ -380,7 +383,10 @@ Example call: \fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR Min fraction of PME nodes to test with .BI "\-npme" " enum" " auto" - Benchmark all possible values for \-npme or just the subset that is expected to perform well: \fB auto\fR, \fB all\fR or \fB subset\fR + Benchmark all possible values for \fB \-npme\fR or just the subset that is expected to perform well: \fB auto\fR, \fB all\fR or \fB subset\fR + +.BI "\-fix" " int" " \-2" + If = \-1, do not vary the number of PME\-only nodes, instead use this fixed value and only vary rcoulomb and the PME grid spacing. .BI "\-upfac" " real" " 1.2 " Upper limit for rcoulomb scaling factor (Note that rcoulomb upscaling results in fourier grid downscaling) @@ -389,19 +395,19 @@ Example call: \fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR Lower limit for rcoulomb scaling factor .BI "\-ntpr" " int" " 0" - Number of tpr files to benchmark. Create these many files with scaling factors ranging from 1.0 to fac. If 1, automatically choose the number of tpr files to test + Number of \fB .tpr\fR files to benchmark. Create this many files with scaling factors ranging from 1.0 to fac. If 1, automatically choose the number of \fB .tpr\fR files to test .BI "\-four" " real" " 0 " - Use this fourierspacing value instead of the grid found in the tpr input file. (Spacing applies to a scaling factor of 1.0 if multiple tpr files are written) + Use this fourierspacing value instead of the grid found in the \fB .tpr\fR input file. (Spacing applies to a scaling factor of 1.0 if multiple \fB .tpr\fR files are written) .BI "\-steps" " step" " 1000" - Take timings for these many steps in the benchmark runs + Take timings for this many steps in the benchmark runs .BI "\-resetstep" " int" " 100" - Let dlb equilibrate these many steps before timings are taken (reset cycle counters after these many steps) + Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps) .BI "\-simsteps" " step" " \-1" - If non\-negative, perform these many steps in the real run (overwrite nsteps from tpr, add cpt steps) + If non\-negative, perform this many steps in the real run (overwrites nsteps from \fB .tpr\fR, add \fB .cpt\fR steps) .BI "\-[no]launch" "no " Lauch the real simulation after optimization @@ -467,7 +473,7 @@ Example call: \fB g_tune_pme \-np 64 \-s protein.tpr \-launch\fR Seed for replica exchange, \-1 is generate a seed .BI "\-[no]ionize" "no " - Do a simulation including the effect of an X\-Ray bombardment on your system + Do a simulation including the effect of an X\-ray bombardment on your system .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_vanhove.1 b/man/man1/g_vanhove.1 index 66df424bc6..c88a6933c1 100644 --- a/man/man1/g_vanhove.1 +++ b/man/man1/g_vanhove.1 @@ -1,8 +1,8 @@ -.TH g_vanhove 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_vanhove - calculates Van Hove displacement functions -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_vanhove\fP .BI "\-f" " traj.xtc " @@ -30,10 +30,10 @@ g_vanhove - calculates Van Hove displacement functions .BI "\-rt" " real " .BI "\-ft" " int " .SH DESCRIPTION -\&g_vanhove computes the Van Hove correlation function. +\&\fB g_vanhove\fR computes the Van Hove correlation function. \&The Van Hove G(r,t) is the probability that a particle that is at r0 \&at time zero can be found at position r0+r at time t. -\&g_vanhove determines G not for a vector r, but for the length of r. +\&\fB g_vanhove\fR determines G not for a vector r, but for the length of r. \&Thus it gives the probability that a particle moves a distance of r \&in time t. \&Jumps across the periodic boundaries are removed. @@ -112,7 +112,7 @@ g_vanhove - calculates Van Hove displacement functions Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -127,7 +127,7 @@ g_vanhove - calculates Van Hove displacement functions Maximum r in the matrix (nm) .BI "\-rbin" " real" " 0.01 " - Binwidth in the matrix and for \-or (nm) + Binwidth in the matrix and for \fB \-or\fR (nm) .BI "\-mmax" " real" " 0 " Maximum density in the matrix, 0 is calculate (1/nm) @@ -136,16 +136,16 @@ g_vanhove - calculates Van Hove displacement functions Number of levels in the matrix .BI "\-nr" " int" " 1" - Number of curves for the \-or output + Number of curves for the \fB \-or\fR output .BI "\-fr" " int" " 0" - Frame spacing for the \-or output + Frame spacing for the \fB \-or\fR output .BI "\-rt" " real" " 0 " - Integration limit for the \-ot output (nm) + Integration limit for the \fB \-ot\fR output (nm) .BI "\-ft" " int" " 0" - Number of frames in the \-ot output, 0 is plot all + Number of frames in the \fB \-ot\fR output, 0 is plot all .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_velacc.1 b/man/man1/g_velacc.1 index 86c4ab831f..a656d115f0 100644 --- a/man/man1/g_velacc.1 +++ b/man/man1/g_velacc.1 @@ -1,8 +1,8 @@ -.TH g_velacc 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_velacc - calculates velocity autocorrelation functions -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_velacc\fP .BI "\-f" " traj.trr " @@ -27,7 +27,7 @@ g_velacc - calculates velocity autocorrelation functions .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&g_velacc computes the velocity autocorrelation function. +\&\fB g_velacc\fR computes the velocity autocorrelation function. \&When the \fB \-m\fR option is used, the momentum autocorrelation \&function is calculated. @@ -72,7 +72,7 @@ g_velacc - calculates velocity autocorrelation functions Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -93,7 +93,7 @@ g_velacc - calculates velocity autocorrelation functions Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" - Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR + Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions diff --git a/man/man1/g_wham.1 b/man/man1/g_wham.1 index 98c591e36c..0adcaa5502 100644 --- a/man/man1/g_wham.1 +++ b/man/man1/g_wham.1 @@ -1,8 +1,8 @@ -.TH g_wham 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_wham - weighted histogram analysis after umbrella sampling -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_wham\fP .BI "\-ix" " pullx\-files.dat " @@ -11,10 +11,11 @@ g_wham - weighted histogram analysis after umbrella sampling .BI "\-ip" " pdo\-files.dat " .BI "\-o" " profile.xvg " .BI "\-hist" " histo.xvg " +.BI "\-oiact" " iact.xvg " +.BI "\-iiact" " iact\-in.dat " .BI "\-bsres" " bsResult.xvg " .BI "\-bsprof" " bsProfs.xvg " .BI "\-tab" " umb\-pot.dat " -.BI "\-wcorr" " cycl\-corr.xvg " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " @@ -34,14 +35,15 @@ g_wham - weighted histogram analysis after umbrella sampling .BI "\-[no]log" "" .BI "\-unit" " enum " .BI "\-zprof0" " real " -.BI "\-cycl" " enum " -.BI "\-alpha" " real " -.BI "\-[no]flip" "" -.BI "\-[no]hist\-eq" "" +.BI "\-[no]cycl" "" +.BI "\-[no]sym" "" +.BI "\-[no]ac" "" +.BI "\-acsig" " real " +.BI "\-ac\-trestart" " real " .BI "\-nBootstrap" " int " -.BI "\-bs\-dt" " real " +.BI "\-bs\-method" " enum " +.BI "\-bs\-tau" " real " .BI "\-bs\-seed" " int " -.BI "\-[no]histbs" "" .BI "\-histbs\-block" " int " .BI "\-[no]vbs" "" .SH DESCRIPTION @@ -51,24 +53,24 @@ g_wham - weighted histogram analysis after umbrella sampling \&compute a potential of mean force (PMF). -\&At present, three input modes are supported: +\&At present, three input modes are supported. \&\fB *\fR With option \fB \-it\fR, the user provides a file which contains the -\& filenames of the umbrella simulation run\-input files (tpr files), -\& AND, with option \-ix, a file which contains filenames of -\& the pullx mdrun output files. The tpr and pullx files must -\& be in corresponding order, i.e. the first tpr created the -\& first pullx, etc. +\& file names of the umbrella simulation run\-input files (\fB .tpr\fR files), +\& AND, with option \fB \-ix\fR, a file which contains file names of +\& the pullx \fB mdrun\fR output files. The \fB .tpr\fR and pullx files must +\& be in corresponding order, i.e. the first \fB .tpr\fR created the +\& first pullx, etc. \&\fB *\fR Same as the previous input mode, except that the the user -\& provides the pull force ouput file names (pullf.xvg) with option \-if. -\& From the pull force the position in the ubrella potential is -\& computed. This does not work with tabulated umbrella potentials. -\&\fB *\fR With option \fB \-ip\fR, the user provides filenames of (gzipped) pdo files, i.e. -\& the gromacs 3.3 umbrella output files. If you have some unusual -\& reaction coordinate you may also generate your own pdo files and -\& feed them with the \-ip option into to g_wham. The pdo file header -\& must be similar to the folowing: +\& provides the pull force output file names (\fB pullf.xvg\fR) with option \fB \-if\fR. +\& From the pull force the position in the umbrella potential is +\& computed. This does not work with tabulated umbrella potentials. +\fB *\fR With option \fB \-ip\fR, the user provides file names of (gzipped) \fB .pdo\fR files, i.e. +\& the GROMACS 3.3 umbrella output files. If you have some unusual reaction coordinate you may also generate your own \fB .pdo\fR files and +\& feed them with the \fB \-ip\fR option into to \fB g_wham\fR. The \fB .pdo\fR file header +\& must be similar to the following: + \&\fB UMBRELLA 3.0 @@ -86,95 +88,134 @@ g_wham - weighted histogram analysis after umbrella sampling \&\fR -\& Nr of pull groups, umbrella positions, force constants, and names -\& may (of course) differ. Following the header, a time column and -\& a data columns for each pull group follow (i.e. the displacement -\& with respect to the umbrella center). Up to four pull groups are possible -\& at present. + +\&The number of pull groups, umbrella positions, force constants, and names +\&may (of course) differ. Following the header, a time column and +\&a data column for each pull group follows (i.e. the displacement +\&with respect to the umbrella center). Up to four pull groups are possible +\&per \fB .pdo\fR file at present. \&By default, the output files are \& \fB \-o\fR PMF output file -\& \fB \-hist\fR histograms output file +\& \fB \-hist\fR Histograms output file + +\&Always check whether the histograms sufficiently overlap. \&The umbrella potential is assumed to be harmonic and the force constants are -\&read from the tpr or pdo files. If a non\-harmonic umbrella force was applied -\&a tabulated potential can be provied with \-tab. +\&read from the \fB .tpr\fR or \fB .pdo\fR files. If a non\-harmonic umbrella force was applied +\&a tabulated potential can be provided with \fB \-tab\fR. \&WHAM OPTIONS +\-\-\-\-\-\-\-\-\-\-\-\- - -\& \fB \-bins\fR Nr of bins used in analysis +\& \fB \-bins\fR Number of bins used in analysis \& \fB \-temp\fR Temperature in the simulations \& \fB \-tol\fR Stop iteration if profile (probability) changed less than tolerance -\& \fB \-auto\fR Automatic determination of boudndaries +\& \fB \-auto\fR Automatic determination of boundaries \& \fB \-min,\-max\fR Boundaries of the profile -\&The data points which are used -\&to compute the profile can be restricted with options \-b, \-e, and \-dt. -\&Play particularly with \-b to ensure sufficient equilibration in each -\&umbrella window! - - -\&With \-log (default) the profile is written in energy units, otherwise (\-nolog) as -\&probability. The unit can be specified with \-unit. With energy output, -\&the energy in the first bin is defined to be zero. If you want the free energy at a different -\&position to be zero, choose with \-zprof0 (useful with bootstrapping, see below). +\&The data points that are used to compute the profile +\&can be restricted with options \fB \-b\fR, \fB \-e\fR, and \fB \-dt\fR. +\&Adjust \fB \-b\fR to ensure sufficient equilibration in each +\&umbrella window. -\&For cyclic (or periodic) reaction coordinates (dihedral angle, channel PMF -\&without osmotic gradient), \-cycl is useful. +\&With \fB \-log\fR (default) the profile is written in energy units, otherwise +\&(with \fB \-nolog\fR) as probability. The unit can be specified with \fB \-unit\fR. +\&With energy output, the energy in the first bin is defined to be zero. +\&If you want the free energy at a different +\&position to be zero, set \fB \-zprof0\fR (useful with bootstrapping, see below). -\&\fB \-cycl yes\fR min and max are assumed to -\&be neighboring points and histogram points outside min and max are mapped into -\&the interval [min,max] (compare histogram output). -\&\fB \-cycl weighted\fR First, a non\-cyclic profile is computed. Subsequently, -\&periodicity is enforced by adding corrections dG(i) between neighboring bins -\&i and i+1. The correction is chosen proportional to 1/[n(i)*n(i+1)]alpha, where -\&n(i) denotes the total nr of data points in bin i as collected from all histograms. -\&alpha is defined with \-alpha. The corrections are written to the file defined by \-wcorr. -\& (Compare Hub and de Groot, PNAS 105:1198 (2008)) +\&For cyclic or periodic reaction coordinates (dihedral angle, channel PMF +\&without osmotic gradient), the option \fB \-cycl\fR is useful. \fB g_wham\fR will make use of the +\&periodicity of the system and generate a periodic PMF. The first and the last bin of the +\&reaction coordinate will assumed be be neighbors. -\&ERROR ANALYSIS - -\&Statistical errors may be estimated with bootstrap analysis. Use it with care, -\&otherwise the statistical error may be substantially undererstimated !! +\&Option \fB \-sym\fR symmetrizes the profile around z=0 before output, +\&which may be useful for, e.g. membranes. -\&\fB \-nBootstrap\fR defines the nr of bootstraps. Two bootstrapping modes are supported. -\&\fB \-histbs\fR Complete histograms are considered as independent data points (default). For each -\&bootstrap, N histograms are randomly chosen from the N given histograms (allowing duplication). -\&To avoid gaps without data along the reaction coordinate blocks of histograms (\-histbs\-block) -\&may be defined. In that case, the given histograms are divided into blocks and -\&only histograms within each block are mixed. Note that the histograms -\&within each block must be representative for all possible histograms, otherwise the -\&statistical error is undererstimated! +\&AUTOCORRELATIONS +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- -\&\fB \-nohistbs\fR The given histograms are used to generate new random histograms, -\&such that the generated data points are distributed according the given histograms. The number -\&of points generated for each bootstrap histogram can be controlled with \-bs\-dt. -\&Note that one data point should be generated for each *independent* point in the given -\&histograms. With the long autocorrelations in MD simulations, this procedure may -\&easily understimate the error! +\&With \fB \-ac\fR, \fB g_wham\fR estimates the integrated autocorrelation +\&time (IACT) [GRK]tau[grk] for each umbrella window and weights the respective +\&window with 1/[1+2*[GRK]tau[grk]/dt]. The IACTs are written +\&to the file defined with \fB \-oiact\fR. In verbose mode, all +\&autocorrelation functions (ACFs) are written to \fB hist_autocorr.xvg\fR. +\&Because the IACTs can be severely underestimated in case of limited +\&sampling, option \fB \-acsig\fR allows to smooth the IACTs along the +\&reaction coordinate with a Gaussian ([GRK]sigma[grk] provided with \fB \-acsig\fR, +\&see output in \fB iact.xvg\fR). Note that the IACTs are estimated by simple +\&integration of the ACFs while the ACFs are larger 0.05. +\&If you prefer to compute the IACTs by a more sophisticated (but possibly +\&less robust) method such as fitting to a double exponential, you can +\&compute the IACTs with \fB g_analyze\fR and provide them to \fB g_wham\fR with the file +\&\fB iact\-in.dat\fR (option \fB \-iiact\fR), which should contain one line per +\&input file (\fB .pdo\fR or pullx/f file) and one column per pull group in the respective file. -\&Bootstrapping output: -\&\fB \-bsres\fR Average profile and standard deviations - -\&\fB \-bsprof\fR All bootstrapping profiles +\&ERROR ANALYSIS +\-\-\-\-\-\-\-\-\-\-\-\-\-\- -\&With \fB \-vbs\fR (verbose bootstrapping), the histograms of each bootstrap are written, and, -\&with \fB \-nohistBS\fR, the cummulants of the histogram. +\&Statistical errors may be estimated with bootstrap analysis. Use it with care, +\&otherwise the statistical error may be substantially underestimated. +\&More background and examples for the bootstrap technique can be found in +\&Hub, de Groot and Van der Spoel, JCTC (2010) 6: 3713\-3720. + +\&\fB \-nBootstrap\fR defines the number of bootstraps (use, e.g., 100). +\&Four bootstrapping methods are supported and +\&selected with \fB \-bs\-method\fR. + +\& (1) \fB b\-hist\fR Default: complete histograms are considered as independent +\&data points, and the bootstrap is carried out by assigning random weights to the +\&histograms ("Bayesian bootstrap"). Note that each point along the reaction coordinate +\&must be covered by multiple independent histograms (e.g. 10 histograms), otherwise the +\&statistical error is underestimated. + +\& (2) \fB hist\fR Complete histograms are considered as independent data points. +\&For each bootstrap, N histograms are randomly chosen from the N given histograms +\&(allowing duplication, i.e. sampling with replacement). +\&To avoid gaps without data along the reaction coordinate blocks of histograms +\&(\fB \-histbs\-block\fR) may be defined. In that case, the given histograms are +\÷d into blocks and only histograms within each block are mixed. Note that +\&the histograms within each block must be representative for all possible histograms, +\&otherwise the statistical error is underestimated. + +\& (3) \fB traj\fR The given histograms are used to generate new random trajectories, +\&such that the generated data points are distributed according the given histograms +\&and properly autocorrelated. The autocorrelation time (ACT) for each window must be +\&known, so use \fB \-ac\fR or provide the ACT with \fB \-iiact\fR. If the ACT of all +\&windows are identical (and known), you can also provide them with \fB \-bs\-tau\fR. +\&Note that this method may severely underestimate the error in case of limited sampling, +\&that is if individual histograms do not represent the complete phase space at +\&the respective positions. + +\& (4) \fB traj\-gauss\fR The same as method \fB traj\fR, but the trajectories are +\¬ bootstrapped from the umbrella histograms but from Gaussians with the average +\&and width of the umbrella histograms. That method yields similar error estimates +\&like method \fB traj\fR. + +Bootstrapping output: + +\& \fB \-bsres\fR Average profile and standard deviations + +\& \fB \-bsprof\fR All bootstrapping profiles + +\&With \fB \-vbs\fR (verbose bootstrapping), the histograms of each bootstrap are written, +\&and, with bootstrap method \fB traj\fR, the cumulative distribution functions of +\&the histograms. .SH FILES .BI "\-ix" " pullx\-files.dat" .B Input, Opt. @@ -200,6 +241,14 @@ g_wham - weighted histogram analysis after umbrella sampling .B Output xvgr/xmgr file +.BI "\-oiact" " iact.xvg" +.B Output, Opt. + xvgr/xmgr file + +.BI "\-iiact" " iact\-in.dat" +.B Input, Opt. + Generic data file + .BI "\-bsres" " bsResult.xvg" .B Output, Opt. xvgr/xmgr file @@ -212,10 +261,6 @@ g_wham - weighted histogram analysis after umbrella sampling .B Input, Opt. Generic data file -.BI "\-wcorr" " cycl\-corr.xvg" -.B Input, Opt. - xvgr/xmgr file - .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit @@ -236,7 +281,7 @@ g_wham - weighted histogram analysis after umbrella sampling Maximum coordinate in profile .BI "\-[no]auto" "yes " - determine min and max automatically + Determine min and max automatically .BI "\-bins" " int" " 200" Number of bins in profile @@ -248,13 +293,13 @@ g_wham - weighted histogram analysis after umbrella sampling Tolerance .BI "\-[no]v" "no " - verbose mode + Verbose mode .BI "\-b" " real" " 50 " - first time to analyse (ps) + First time to analyse (ps) .BI "\-e" " real" " 1e+20 " - last time to analyse (ps) + Last time to analyse (ps) .BI "\-dt" " real" " 0 " Analyse only every dt ps @@ -263,46 +308,49 @@ g_wham - weighted histogram analysis after umbrella sampling Write histograms and exit .BI "\-[no]boundsonly" "no " - Determine min and max and exit (with \-auto) + Determine min and max and exit (with \fB \-auto\fR) .BI "\-[no]log" "yes " Calculate the log of the profile before printing .BI "\-unit" " enum" " kJ" - energy unit in case of log output: \fB kJ\fR, \fB kCal\fR or \fB kT\fR + Energy unit in case of log output: \fB kJ\fR, \fB kCal\fR or \fB kT\fR .BI "\-zprof0" " real" " 0 " - Define profile to 0.0 at this position (with \-log) + Define profile to 0.0 at this position (with \fB \-log\fR) -.BI "\-cycl" " enum" " no" - Create cyclic/periodic profile. Assumes min and max are the same point.: \fB no\fR, \fB yes\fR or \fB weighted\fR +.BI "\-[no]cycl" "no " + Create cyclic/periodic profile. Assumes min and max are the same point. -.BI "\-alpha" " real" " 2 " - for '\-cycl weighted', set parameter alpha +.BI "\-[no]sym" "no " + Symmetrize profile around z=0 -.BI "\-[no]flip" "no " - Combine halves of profile (not supported) +.BI "\-[no]ac" "no " + Calculate integrated autocorrelation times and use in wham -.BI "\-[no]hist\-eq" "no " - Enforce equal weight for all histograms. (Non\-Weighed\-HAM) +.BI "\-acsig" " real" " 0 " + Smooth autocorrelation times along reaction coordinate with Gaussian of this [GRK]sigma[grk] + +.BI "\-ac\-trestart" " real" " 1 " + When computing autocorrelation functions, restart computing every .. (ps) .BI "\-nBootstrap" " int" " 0" - nr of bootstraps to estimate statistical uncertainty + nr of bootstraps to estimate statistical uncertainty (e.g., 200) -.BI "\-bs\-dt" " real" " 0 " - timestep for synthetic bootstrap histograms (ps). Ensure independent data points! +.BI "\-bs\-method" " enum" " b\-hist" + Bootstrap method: \fB b\-hist\fR, \fB hist\fR, \fB traj\fR or \fB traj\-gauss\fR -.BI "\-bs\-seed" " int" " \-1" - seed for bootstrapping. (\-1 = use time) +.BI "\-bs\-tau" " real" " 0 " + Autocorrelation time (ACT) assumed for all histograms. Use option \fB \-ac\fR if ACT is unknown. -.BI "\-[no]histbs" "yes " - In bootstrapping, consider complete histograms as one data point. Accounts better for long autocorrelations. +.BI "\-bs\-seed" " int" " \-1" + Seed for bootstrapping. (\-1 = use time) .BI "\-histbs\-block" " int" " 8" - when mixin histograms only mix within blocks of \-histBS_block. + When mixing histograms only mix within blocks of \fB \-histbs\-block\fR. .BI "\-[no]vbs" "no " - verbose bootstrapping. Print the cummulants and a histogram file for each bootstrap. + Verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap. .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_wheel.1 b/man/man1/g_wheel.1 index 7d90b5cbd4..5207ea39a3 100644 --- a/man/man1/g_wheel.1 +++ b/man/man1/g_wheel.1 @@ -1,8 +1,8 @@ -.TH g_wheel 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_wheel - plots helical wheels -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_wheel\fP .BI "\-f" " nnnice.dat " @@ -15,9 +15,9 @@ g_wheel - plots helical wheels .BI "\-T" " string " .BI "\-[no]nn" "" .SH DESCRIPTION -\&wheel plots a helical wheel representation of your sequence. -\&The input sequence is in the .dat file where the first line contains -\&the number of residues and each consecutive line contains a residuename. +\&\fB g_wheel\fR plots a helical wheel representation of your sequence. +\&The input sequence is in the \fB .dat\fR file where the first line contains +\&the number of residues and each consecutive line contains a residue name. .SH FILES .BI "\-f" " nnnice.dat" .B Input diff --git a/man/man1/g_x2top.1 b/man/man1/g_x2top.1 index 321bb878a6..5bb14a22e1 100644 --- a/man/man1/g_x2top.1 +++ b/man/man1/g_x2top.1 @@ -1,8 +1,8 @@ -.TH g_x2top 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_x2top - generates a primitive topology from coordinates -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_x2top\fP .BI "\-f" " conf.gro " @@ -27,11 +27,11 @@ g_x2top - generates a primitive topology from coordinates .BI "\-kt" " real " .BI "\-kp" " real " .SH DESCRIPTION -\&x2top generates a primitive topology from a coordinate file. +\&\fB g_x2top\fR generates a primitive topology from a coordinate file. \&The program assumes all hydrogens are present when defining \&the hybridization from the atom name and the number of bonds. -\&The program can also make an rtp entry, which you can then add -\&to the rtp database. +\&The program can also make an \fB .rtp\fR entry, which you can then add +\&to the \fB .rtp\fR database. \&When \fB \-param\fR is set, equilibrium distances and angles @@ -49,11 +49,11 @@ g_x2top - generates a primitive topology from coordinates \&The corresponding data files can be found in the library directory -\&with name atomname2type.n2t. Check chapter 5 of the manual for more -\&information about file formats. By default the forcefield selection +\&with name \fB atomname2type.n2t\fR. Check Chapter 5 of the manual for more +\&information about file formats. By default, the force field selection \&is interactive, but you can use the \fB \-ff\fR option to specify \&one of the short names above on the command line instead. In that -\&case pdb2gmx just looks for the corresponding file. +\&case \fB g_x2top\fR just looks for the corresponding file. .SH FILES @@ -107,7 +107,7 @@ g_x2top - generates a primitive topology from coordinates Use periodic boundary conditions. .BI "\-[no]pdbq" "no " - Use the B\-factor supplied in a pdb file for the atomic charges + Use the B\-factor supplied in a \fB .pdb\fR file for the atomic charges .BI "\-[no]param" "yes " Print parameters in the output @@ -131,7 +131,7 @@ g_x2top - generates a primitive topology from coordinates \- No improper dihedrals are generated -\- The atoms to atomtype translation table is incomplete (atomname2type.n2t files in the data directory). Please extend it and send the results back to the GROMACS crew. +\- The atoms to atomtype translation table is incomplete (\fB atomname2type.n2t\fR file in the data directory). Please extend it and send the results back to the GROMACS crew. .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/g_xrama.1 b/man/man1/g_xrama.1 index c0c0efcba0..e0360b3949 100644 --- a/man/man1/g_xrama.1 +++ b/man/man1/g_xrama.1 @@ -1,8 +1,8 @@ -.TH g_xrama 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME g_xrama - shows animated Ramachandran plots -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3g_xrama\fP .BI "\-f" " traj.xtc " @@ -14,15 +14,15 @@ g_xrama - shows animated Ramachandran plots .BI "\-e" " time " .BI "\-dt" " time " .SH DESCRIPTION -\&xrama shows a Ramachandran movie, that is, it shows +\&\fB g_xrama\fR shows a Ramachandran movie, that is, it shows \&the Phi/Psi angles as a function of time in an X\-Window. -Static Phi/Psi plots for printing can be made with g_rama. +Static Phi/Psi plots for printing can be made with \fB g_rama\fR. \&Some of the more common X command line options can be used: -\&\-bg, \-fg change colors, \-font fontname, changes the font. +\&\fB \-bg\fR, \fB \-fg\fR change colors, \fB \-font fontname\fR, changes the font. .SH FILES .BI "\-f" " traj.xtc" .B Input diff --git a/man/man1/genbox.1 b/man/man1/genbox.1 index d3744047a2..2ec3d33b73 100644 --- a/man/man1/genbox.1 +++ b/man/man1/genbox.1 @@ -1,8 +1,8 @@ -.TH genbox 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME genbox - solvates a system -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3genbox\fP .BI "\-cp" " protein.gro " @@ -22,14 +22,14 @@ genbox - solvates a system .BI "\-maxsol" " int " .BI "\-[no]vel" "" .SH DESCRIPTION -\&Genbox can do one of 3 things: +\&\fB genbox\fR can do one of 3 things: -\&1) Generate a box of solvent. Specify \-cs and \-box. Or specify \-cs and -\&\-cp with a structure file with a box, but without atoms. +\&1) Generate a box of solvent. Specify \fB \-cs\fR and \fB \-box\fR. Or specify \fB \-cs\fR and +\&\fB \-cp\fR with a structure file with a box, but without atoms. -\&2) Solvate a solute configuration, eg. a protein, in a bath of solvent +\&2) Solvate a solute configuration, e.g. a protein, in a bath of solvent \&molecules. Specify \fB \-cp\fR (solute) and \fB \-cs\fR (solvent). \&The box specified in the solute coordinate file (\fB \-cp\fR) is used, \&unless \fB \-box\fR is set. @@ -38,9 +38,9 @@ genbox - solvates a system \&to change the box dimensions and center the solute. \&Solvent molecules are removed from the box where the \&distance between any atom of the solute molecule(s) and any atom of -\&the solvent molecule is less than the sum of the VanderWaals radii of -\&both atoms. A database (\fB vdwradii.dat\fR) of VanderWaals radii is -\&read by the program, atoms not in the database are +\&the solvent molecule is less than the sum of the van der Waals radii of +\&both atoms. A database (\fB vdwradii.dat\fR) of van der Waals radii is +\&read by the program, and atoms not in the database are \&assigned a default distance \fB \-vdwd\fR. \&Note that this option will also influence the distances between \&solvent molecules if they contain atoms that are not in the database. @@ -51,11 +51,16 @@ genbox - solvates a system \&at random positions. \&The program iterates until \fB nmol\fR molecules \&have been inserted in the box. To test whether an insertion is -\&successful the same VanderWaals criterium is used as for removal of -\&solvent molecules. When no appropriately -\&sized holes (holes that can hold an extra molecule) are available the +\&successful the same van der Waals criterium is used as for removal of +\&solvent molecules. When no appropriately\-sized +\&holes (holes that can hold an extra molecule) are available, the \&program tries for \fB \-nmol\fR * \fB \-try\fR times before giving up. -\&Increase \-try if you have several small holes to fill. +\&Increase \fB \-try\fR if you have several small holes to fill. + + +\&If you need to do more than one of the above operations, it can be +\&best to call \fB genbox\fR separately for each operation, so that +\&you are sure of the order in which the operations occur. \&The default solvent is Simple Point Charge water (SPC), with coordinates @@ -81,18 +86,18 @@ genbox - solvates a system \&longest molecule axis along a box edge. This way the amount of solvent \&molecules necessary is reduced. \&It should be kept in mind that this only works for -\&short simulations, as eg. an alpha\-helical peptide in solution can +\&short simulations, as e.g. an alpha\-helical peptide in solution can \&rotate over 90 degrees, within 500 ps. In general it is therefore \&better to make a more or less cubic box. -\&Setting \-shell larger than zero will place a layer of water of +\&Setting \fB \-shell\fR larger than zero will place a layer of water of \&the specified thickness (nm) around the solute. Hint: it is a good -\&idea to put the protein in the center of a box first (using editconf). +\&idea to put the protein in the center of a box first (using \fB editconf\fR). \& -\&Finally, genbox will optionally remove lines from your topology file in +\&Finally, \fB genbox\fR will optionally remove lines from your topology file in \&which a number of solvent molecules is already added, and adds a \&line with the total number of solvent molecules in your coordinate file. .SH FILES @@ -133,7 +138,7 @@ genbox - solvates a system no of extra molecules to insert .BI "\-try" " int" " 10" - try inserting \-nmol*\-try times + try inserting \fB \-nmol\fR times \fB \-try\fR times .BI "\-seed" " int" " 1997" random generator seed diff --git a/man/man1/genconf.1 b/man/man1/genconf.1 index 9757dbca77..85a8d6d780 100644 --- a/man/man1/genconf.1 +++ b/man/man1/genconf.1 @@ -1,8 +1,8 @@ -.TH genconf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME genconf - multiplies a conformation in 'random' orientations -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3genconf\fP .BI "\-f" " conf.gro " @@ -22,9 +22,9 @@ genconf - multiplies a conformation in 'random' orientations .BI "\-maxrot" " vector " .BI "\-[no]renumber" "" .SH DESCRIPTION -\&genconf multiplies a given coordinate file by simply stacking them +\&\fB genconf\fR multiplies a given coordinate file by simply stacking them \&on top of each other, like a small child playing with wooden blocks. -\&The program makes a grid of \fI user defined\fR +\&The program makes a grid of \fI user\-defined\fR \&proportions (\fB \-nbox\fR), \&and interspaces the grid point with an extra space \fB \-dist\fR. @@ -32,7 +32,7 @@ genconf - multiplies a conformation in 'random' orientations \&When option \fB \-rot\fR is used the program does not check for overlap \&between molecules on grid points. It is recommended to make the box in \&the input file at least as big as the coordinates + -\&Van der Waals radius. +\&van der Waals radius. \&If the optional trajectory file is given, conformations are not diff --git a/man/man1/genion.1 b/man/man1/genion.1 index bc535a2336..6cb4dcf8e9 100644 --- a/man/man1/genion.1 +++ b/man/man1/genion.1 @@ -1,8 +1,8 @@ -.TH genion 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME genion - generates mono atomic ions on energetically favorable positions -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3genion\fP .BI "\-s" " topol.tpr " @@ -29,10 +29,10 @@ genion - generates mono atomic ions on energetically favorable positions .BI "\-conc" " real " .BI "\-[no]neutral" "" .SH DESCRIPTION -\&genion replaces solvent molecules by monoatomic ions at +\&\fB genion\fR replaces solvent molecules by monoatomic ions at \&the position of the first atoms with the most favorable electrostatic \&potential or at random. The potential is calculated on all atoms, using -\&normal GROMACS particle based methods (in contrast to other methods +\&normal GROMACS particle\-based methods (in contrast to other methods \&based on solving the Poisson\-Boltzmann equation). \&The potential is recalculated after every ion insertion. \&If specified in the run input file, a reaction field, shift function @@ -45,18 +45,23 @@ genion - generates mono atomic ions on energetically favorable positions \&The ion molecule type, residue and atom names in all force fields -\&are the capitalized element names without sign. Ions which can have -\&multiple charge states get the multiplicilty added, without sign, -\&for the uncommon states only. +\&are the capitalized element names without sign. This molecule name +\&should be given with \fB \-pname\fR or \fB \-nname\fR, and the +\&\fB [molecules]\fR section of your topology updated accordingly, +\&either by hand or with \fB \-p\fR. Do not use an atom name instead! +\& + +Ions which can have multiple charge states get the multiplicity +\&added, without sign, for the uncommon states only. \&With the option \fB \-pot\fR the potential can be written as B\-factors -\&in a pdb file (for visualisation using e.g. rasmol). +\&in a \fB .pdb\fR file (for visualisation using e.g. Rasmol). \&The unit of the potential is 1000 kJ/(mol e), the scaling be changed \&with the \fB \-scale\fR option. -\&For larger ions, e.g. sulfate we recommended to use genbox. +\&For larger ions, e.g. sulfate we recommended using \fB genbox\fR. .SH FILES .BI "\-s" " topol.tpr" .B Input @@ -127,10 +132,10 @@ genion - generates mono atomic ions on energetically favorable positions Seed for random number generator .BI "\-scale" " real" " 0.001 " - Scaling factor for the potential for \-pot + Scaling factor for the potential for \fB \-pot\fR .BI "\-conc" " real" " 0 " - Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the \-np and nn options. + Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input \fB .tpr\fR file. Overrides the \fB \-np\fR and \fB \-nn\fR options. .BI "\-[no]neutral" "no " This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. diff --git a/man/man1/genrestr.1 b/man/man1/genrestr.1 index 68cc920169..37992dce4e 100644 --- a/man/man1/genrestr.1 +++ b/man/man1/genrestr.1 @@ -1,8 +1,8 @@ -.TH genrestr 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME genrestr - generates position restraints or distance restraints for index groups -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3genrestr\fP .BI "\-f" " conf.gro " @@ -21,9 +21,9 @@ genrestr - generates position restraints or distance restraints for index groups .BI "\-cutoff" " real " .BI "\-[no]constr" "" .SH DESCRIPTION -\&genrestr produces an include file for a topology containing +\&\fB genrestr\fR produces an include file for a topology containing \&a list of atom numbers and three force constants for the -\&X, Y and Z direction. A single isotropic force constant may +\&\fI x\fR\-, \fI y\fR\-, and \fI z\fR\-direction. A single isotropic force constant may \&be given on the command line instead of three components. @@ -32,17 +32,17 @@ genrestr - generates position restraints or distance restraints for index groups \&they should be included within the correct \fB [ moleculetype ]\fR \&block in the topology. Since the atom numbers in every moleculetype \&in the topology start at 1 and the numbers in the input file for -\&genpr number consecutively from 1, genpr will only produce a useful -\&file for the first molecule. +\&\fB genrestr\fR number consecutively from 1, \fB genrestr\fR will only +\&produce a useful file for the first molecule. -\&The \-of option produces an index file that can be used for -\&freezing atoms. In this case the input file must be a pdb file. +\&The \fB \-of\fR option produces an index file that can be used for +\&freezing atoms. In this case, the input file must be a \fB .pdb\fR file. -\&With the \fB \-disre\fR option half a matrix of distance restraints +\&With the \fB \-disre\fR option, half a matrix of distance restraints \&is generated instead of position restraints. With this matrix, that -\&one typically would apply to C\-alpha atoms in a protein, one can +\&one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can \&maintain the overall conformation of a protein without tieing it to \&a specific position (as with position restraints). .SH FILES @@ -73,10 +73,10 @@ genrestr - generates position restraints or distance restraints for index groups Set the nicelevel .BI "\-fc" " vector" " 1000 1000 1000" - force constants (kJ mol\-1 nm\-2) + force constants (kJ/mol nm2) .BI "\-freeze" " real" " 0 " - if the \-of option or this one is given an index file will be written containing atom numbers of all atoms that have a B\-factor less than the level given here + if the \fB \-of\fR option or this one is given an index file will be written containing atom numbers of all atoms that have a B\-factor less than the level given here .BI "\-[no]disre" "no " Generate a distance restraint matrix for all the atoms in index diff --git a/man/man1/gmxcheck.1 b/man/man1/gmxcheck.1 index 157080fa33..4eb4b6fb4c 100644 --- a/man/man1/gmxcheck.1 +++ b/man/man1/gmxcheck.1 @@ -1,8 +1,8 @@ -.TH gmxcheck 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME gmxcheck - checks and compares files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3gmxcheck\fP .BI "\-f" " traj.xtc " @@ -26,7 +26,7 @@ gmxcheck - checks and compares files .BI "\-[no]ab" "" .BI "\-lastener" " string " .SH DESCRIPTION -\&gmxcheck reads a trajectory (\fB .trj\fR, \fB .trr\fR or +\&\fB gmxcheck\fR reads a trajectory (\fB .trj\fR, \fB .trr\fR or \&\fB .xtc\fR), an energy file (\fB .ene\fR or \fB .edr\fR) \&or an index file (\fB .ndx\fR) \&and prints out useful information about them. @@ -44,11 +44,11 @@ gmxcheck - checks and compares files \&If an index file, is given its contents will be summarized. -\&If both a trajectory and a tpr file are given (with \fB \-s1\fR) +\&If both a trajectory and a \fB .tpr\fR file are given (with \fB \-s1\fR) \&the program will check whether the bond lengths defined in the tpr \&file are indeed correct in the trajectory. If not you may have \&non\-matching files due to e.g. deshuffling or due to problems with -\&virtual sites. With these flags, gmxcheck provides a quick check for such problems. +\&virtual sites. With these flags, \fB gmxcheck\fR provides a quick check for such problems. \&The program can compare two run input (\fB .tpr\fR, \fB .tpb\fR or diff --git a/man/man1/gmxdump.1 b/man/man1/gmxdump.1 index a1d44428f9..2be6f6cd58 100644 --- a/man/man1/gmxdump.1 +++ b/man/man1/gmxdump.1 @@ -1,8 +1,8 @@ -.TH gmxdump 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME gmxdump - makes binary files human readable -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3gmxdump\fP .BI "\-s" " topol.tpr " @@ -18,7 +18,7 @@ gmxdump - makes binary files human readable .BI "\-[no]nr" "" .BI "\-[no]sys" "" .SH DESCRIPTION -\&gmxdump reads a run input file (\fB .tpa\fR/\fB .tpr\fR/\fB .tpb\fR), +\&\fB gmxdump\fR reads a run input file (\fB .tpa\fR/\fB .tpr\fR/\fB .tpb\fR), \&a trajectory (\fB .trj\fR/\fB .trr\fR/\fB .xtc\fR), an energy \&file (\fB .ene\fR/\fB .edr\fR), or a checkpoint file (\fB .cpt\fR) \&and prints that to standard output in a readable format. @@ -27,7 +27,7 @@ gmxdump - makes binary files human readable \&The program can also preprocess a topology to help finding problems. -\&Note that currently setting GMXLIB is the only way to customize +\&Note that currently setting \fB GMXLIB\fR is the only way to customize \&directories used for searching include files. .SH FILES .BI "\-s" " topol.tpr" diff --git a/man/man1/grompp.1 b/man/man1/grompp.1 index 016ce3e53d..f6221e3e2b 100644 --- a/man/man1/grompp.1 +++ b/man/man1/grompp.1 @@ -1,8 +1,8 @@ -.TH grompp 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME grompp - makes a run input file -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3grompp\fP .BI "\-f" " grompp.mdp " @@ -37,7 +37,7 @@ grompp - makes a run input file \&for hydrogens and heavy atoms. \&Then a coordinate file is read and velocities can be generated \&from a Maxwellian distribution if requested. -\&grompp also reads parameters for the mdrun +\&\fB grompp\fR also reads parameters for the \fB mdrun\fR \&(eg. number of MD steps, time step, cut\-off), and others such as \&NEMD parameters, which are corrected so that the net acceleration \&is zero. @@ -45,15 +45,16 @@ grompp - makes a run input file \&file for the MD program. -\&grompp uses the atom names from the topology file. The atom names +\&\fB grompp\fR uses the atom names from the topology file. The atom names \&in the coordinate file (option \fB \-c\fR) are only read to generate \&warnings when they do not match the atom names in the topology. \&Note that the atom names are irrelevant for the simulation as \&only the atom types are used for generating interaction parameters. -\&grompp uses a built\-in preprocessor to resolve includes, macros -\&etcetera. The preprocessor supports the following keywords: +\&\fB grompp\fR uses a built\-in preprocessor to resolve includes, macros, +\&etc. The preprocessor supports the following keywords: + \&ifdef VARIABLE @@ -70,24 +71,20 @@ include "filename" \&include filename + \&The functioning of these statements in your topology may be modulated by -\&using the following two flags in your \fB mdp\fR file: +\&using the following two flags in your \fB .mdp\fR file: -\&define = \-DVARIABLE1 \-DVARIABLE2 -\&include = /home/john/doe +\&\fB define = \-DVARIABLE1 \-DVARIABLE2 + +\&include = \-I/home/john/doe\fR \&For further information a C\-programming textbook may help you out. \&Specifying the \fB \-pp\fR flag will get the pre\-processed \&topology file written out so that you can verify its contents. -\&If your system does not have a c\-preprocessor, you can still -\&use grompp, but you do not have access to the features -\&from the cpp. Command line options to the c\-preprocessor can be given -\&in the \fB .mdp\fR file. See your local manual (man cpp). - - \&When using position restraints a file with restraint coordinates \&can be supplied with \fB \-r\fR, otherwise restraining will be done \&with respect to the conformation from the \fB \-c\fR option. @@ -98,26 +95,26 @@ include "filename" \&Starting coordinates can be read from trajectory with \fB \-t\fR. \&The last frame with coordinates and velocities will be read, -\&unless the \fB \-time\fR option is used. +\&unless the \fB \-time\fR option is used. Only if this information +\&is absent will the coordinates in the \fB \-c\fR file be used. \&Note that these velocities will not be used when \fB gen_vel = yes\fR \&in your \fB .mdp\fR file. An energy file can be supplied with \&\fB \-e\fR to read Nose\-Hoover and/or Parrinello\-Rahman coupling -\&variables. Note that for continuation it is better and easier to supply -\&a checkpoint file directly to mdrun, since that always contains -\&the complete state of the system and you don't need to generate -\&a new run input file. Note that if you only want to change the number -\&of run steps tpbconv is more convenient than grompp. +\&variables. -\&Using the \fB \-morse\fR option grompp can convert the harmonic bonds -\&in your topology to morse potentials. This makes it possible to break -\&bonds. For this option to work you need an extra file in your $GMXLIB -\&with dissociation energy. Use the \-debug option to get more information -\&on the workings of this option (look for MORSE in the grompp.log file -\&using less or something like that). +\&\fB grompp\fR can be used to restart simulations (preserving +\&continuity) by supplying just a checkpoint file with \fB \-t\fR. +\&However, for simply changing the number of run steps to extend +\&a run, using \fB tpbconv\fR is more convenient than \fB grompp\fR. +\&You then supply the old checkpoint file directly to \fB mdrun\fR +\&with \fB \-cpi\fR. If you wish to change the ensemble or things +\&like output frequency, then supplying the checkpoint file to +\&\fB grompp\fR with \fB \-t\fR along with a new \fB .mdp\fR file +\&with \fB \-f\fR is the recommended procedure. -\&By default all bonded interactions which have constant energy due to +\&By default, all bonded interactions which have constant energy due to \&virtual site constructions will be removed. If this constant energy is \¬ zero, this will result in a shift in the total energy. All bonded \&interactions can be kept by turning off \fB \-rmvsbds\fR. Additionally, @@ -125,17 +122,24 @@ include "filename" \&of virtual site constructions will be removed. If any constraints remain \&which involve virtual sites, a fatal error will result. -To verify your run input file, please make notice of all warnings +To verify your run input file, please take note of all warnings \&on the screen, and correct where necessary. Do also look at the contents -\&of the \fB mdout.mdp\fR file, this contains comment lines, as well as -\&the input that \fB grompp\fR has read. If in doubt you can start grompp +\&of the \fB mdout.mdp\fR file; this contains comment lines, as well as +\&the input that \fB grompp\fR has read. If in doubt, you can start \fB grompp\fR \&with the \fB \-debug\fR option which will give you more information -\&in a file called grompp.log (along with real debug info). Finally, you +\&in a file called \fB grompp.log\fR (along with real debug info). You \&can see the contents of the run input file with the \fB gmxdump\fR -\&program. +\&program. \fB gmxcheck\fR can be used to compare the contents of two +\&run input files. + +The \fB \-maxwarn\fR option can be used to override warnings printed +\&by \fB grompp\fR that otherwise halt output. In some cases, warnings are +\&harmless, but usually they are not. The user is advised to carefully +\&interpret the output messages before attempting to bypass them with +\&this option. .SH FILES .BI "\-f" " grompp.mdp" -.B Input, Opt. +.B Input grompp input file with MD parameters .BI "\-po" " mdout.mdp" @@ -198,7 +202,7 @@ To verify your run input file, please make notice of all warnings Remove constant bonded interactions with virtual sites .BI "\-maxwarn" " int" " 0" - Number of allowed warnings during input processing + Number of allowed warnings during input processing. Not for normal use and may generate unstable systems .BI "\-[no]zero" "no " Set parameters for bonded interactions without defaults to zero instead of generating an error diff --git a/man/man1/make_edi.1 b/man/man1/make_edi.1 index 3000608e53..e81709f178 100644 --- a/man/man1/make_edi.1 +++ b/man/man1/make_edi.1 @@ -1,8 +1,8 @@ -.TH make_edi 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME make_edi - generate input files for essential dynamics sampling -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3make_edi\fP .BI "\-f" " eigenvec.trr " @@ -19,28 +19,29 @@ make_edi - generate input files for essential dynamics sampling .BI "\-mon" " string " .BI "\-linfix" " string " .BI "\-linacc" " string " -.BI "\-flood" " string " .BI "\-radfix" " string " .BI "\-radacc" " string " .BI "\-radcon" " string " +.BI "\-flood" " string " .BI "\-outfrq" " int " .BI "\-slope" " real " +.BI "\-linstep" " string " +.BI "\-accdir" " string " +.BI "\-radstep" " real " .BI "\-maxedsteps" " int " +.BI "\-eqsteps" " int " .BI "\-deltaF0" " real " .BI "\-deltaF" " real " .BI "\-tau" " real " -.BI "\-eqsteps" " int " .BI "\-Eflnull" " real " .BI "\-T" " real " .BI "\-alpha" " real " -.BI "\-linstep" " string " -.BI "\-accdir" " string " -.BI "\-radstep" " real " .BI "\-[no]restrain" "" .BI "\-[no]hessian" "" .BI "\-[no]harmonic" "" +.BI "\-constF" " string " .SH DESCRIPTION -\&\fB make_edi\fR generates an essential dynamics (ED) sampling input file to be used with mdrun +\&\fB make_edi\fR generates an essential dynamics (ED) sampling input file to be used with \fB mdrun\fR \&based on eigenvectors of a covariance matrix (\fB g_covar\fR) or from a \&normal modes anaysis (\fB g_nmeig\fR). \&ED sampling can be used to manipulate the position along collective coordinates @@ -67,7 +68,7 @@ make_edi - generate input files for essential dynamics sampling \&B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; \&An extended sampling of the configurational space of HPr from E. coli -\&PROTEINS: Struct. Funct. Gen. 26: 314\-322 (1996) +\&Proteins: Struct. Funct. Gen. 26: 314\-322 (1996) \& You will be prompted for one or more index groups that correspond to the eigenvectors, @@ -89,7 +90,7 @@ You will be prompted for one or more index groups that correspond to the eigenve \&\fB \-radacc\fR: perform acceptance radius expansion along selected eigenvectors. \&(steps in the desired direction will be accepted, others will be rejected). -\&Note: by default the starting MD structure will be taken as origin of the first +\&\fB Note:\fR by default the starting MD structure will be taken as origin of the first \&expansion cycle for radius expansion. If \fB \-ori\fR is specified, you will be able \&to read in a structure file that defines an external origin. @@ -101,7 +102,7 @@ You will be prompted for one or more index groups that correspond to the eigenve \&NOTE: each eigenvector can be selected only once. -\&\fB \-outfrq\fR: frequency (in steps) of writing out projections etc. to .edo file +\&\fB \-outfrq\fR: frequency (in steps) of writing out projections etc. to \fB .edo\fR file \&\fB \-slope\fR: minimal slope in acceptance radius expansion. A new expansion @@ -116,21 +117,21 @@ You will be prompted for one or more index groups that correspond to the eigenve \&Note on the parallel implementation: since ED sampling is a 'global' thing \&(collective coordinates etc.), at least on the 'protein' side, ED sampling \&is not very parallel\-friendly from an implentation point of view. Because -\¶llel ED requires much extra communication, expect the performance to be +\¶llel ED requires some extra communication, expect the performance to be \&lower as in a free MD simulation, especially on a large number of nodes. -\&All output of mdrun (specify with \-eo) is written to a .edo file. In the output +\&All output of \fB mdrun\fR (specify with \fB \-eo\fR) is written to a .edo file. In the output \&file, per OUTFRQ step the following information is present: -\&* the step number +\&\fB *\fR the step number -\&* the number of the ED dataset. (Note that you can impose multiple ED constraints in -\&a single simulation \- on different molecules e.g. \- if several .edi files were concatenated -\&first. The constraints are applied in the order they appear in the .edi file.) +\&\fB *\fR the number of the ED dataset. (\fB Note\fR that you can impose multiple ED constraints in +\&a single simulation (on different molecules) if several \fB .edi\fR files were concatenated +\&first. The constraints are applied in the order they appear in the \fB .edi\fR file.) -\&* RMSD (for atoms involved in fitting prior to calculating the ED constraints) +\&\fB *\fR RMSD (for atoms involved in fitting prior to calculating the ED constraints) \&* projections of the positions onto selected eigenvectors @@ -142,34 +143,34 @@ You will be prompted for one or more index groups that correspond to the eigenve \&FLOODING: -\&with \-flood you can specify which eigenvectors are used to compute a flooding potential, +\&with \fB \-flood\fR, you can specify which eigenvectors are used to compute a flooding potential, \&which will lead to extra forces expelling the structure out of the region described \&by the covariance matrix. If you switch \-restrain the potential is inverted and the structure \&is kept in that region. \& -\&The origin is normally the average structure stored in the eigvec.trr file. -\&It can be changed with \-ori to an arbitrary position in configurational space. -\&With \-tau, \-deltaF0 and \-Eflnull you control the flooding behaviour. +\&The origin is normally the average structure stored in the \fB eigvec.trr\fR file. +\&It can be changed with \fB \-ori\fR to an arbitrary position in configurational space. +\&With \fB \-tau\fR, \fB \-deltaF0\fR, and \fB \-Eflnull\fR you control the flooding behaviour. \&Efl is the flooding strength, it is updated according to the rule of adaptive flooding. -\&Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth). +\&Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). \&DeltaF0 is the flooding strength you want to reach after tau ps of simulation. -\&To use constant Efl set \-tau to zero. +\&To use constant Efl set \fB \-tau\fR to zero. \& -\&\-alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found +\&\fB \-alpha\fR is a fudge parameter to control the width of the flooding potential. A value of 2 has been found \&to give good results for most standard cases in flooding of proteins. -\&Alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would -\&increase, this is mimicked by alpha1. -\&For restraining alpha1 can give you smaller width in the restraining potential. +\&[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would +\&increase, this is mimicked by [GRK]alpha[grk] 1. +\&For restraining, [GRK]alpha[grk] 1 can give you smaller width in the restraining potential. \& \&RESTART and FLOODING: \&If you want to restart a crashed flooding simulation please find the values deltaF and Efl in -\&the output file and manually put them into the .edi file under DELTA_F0 and EFL_NULL. +\&the output file and manually put them into the \fB .edi\fR file under DELTA_F0 and EFL_NULL. .SH FILES .BI "\-f" " eigenvec.trr" .B Input @@ -221,9 +222,6 @@ You will be prompted for one or more index groups that correspond to the eigenve .BI "\-linacc" " string" " " Indices of eigenvectors for acceptance linear sampling -.BI "\-flood" " string" " " - Indices of eigenvectors for flooding - .BI "\-radfix" " string" " " Indices of eigenvectors for fixed increment radius expansion @@ -233,29 +231,41 @@ You will be prompted for one or more index groups that correspond to the eigenve .BI "\-radcon" " string" " " Indices of eigenvectors for acceptance radius contraction +.BI "\-flood" " string" " " + Indices of eigenvectors for flooding + .BI "\-outfrq" " int" " 100" - Freqency (in steps) of writing output in .edo file + Freqency (in steps) of writing output in \fB .edo\fR file .BI "\-slope" " real" " 0 " Minimal slope in acceptance radius expansion +.BI "\-linstep" " string" " " + Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 \-3.1") + +.BI "\-accdir" " string" " " + Directions for acceptance linear sampling \- only sign counts! (put in quotes! "\-1 +1 \-1.1") + +.BI "\-radstep" " real" " 0 " + Stepsize (nm/step) for fixed increment radius expansion + .BI "\-maxedsteps" " int" " 0" - Max nr of steps per cycle + Maximum number of steps per cycle + +.BI "\-eqsteps" " int" " 0" + Number of steps to run without any perturbations .BI "\-deltaF0" " real" " 150 " - Target destabilization energy \- used for flooding + Target destabilization energy for flooding .BI "\-deltaF" " real" " 0 " - Start deltaF with this parameter \- default 0, i.e. nonzero values only needed for restart + Start deltaF with this parameter \- default 0, nonzero values only needed for restart .BI "\-tau" " real" " 0.1 " Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength -.BI "\-eqsteps" " int" " 0" - Number of steps to run without any perturbations - .BI "\-Eflnull" " real" " 0 " - This is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use \-tau 0. + The starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. For a constant flooding strength use \fB \-tau\fR 0. .BI "\-T" " real" " 300 " T is temperature, the value is needed if you want to do flooding @@ -263,15 +273,6 @@ You will be prompted for one or more index groups that correspond to the eigenve .BI "\-alpha" " real" " 1 " Scale width of gaussian flooding potential with alpha2 -.BI "\-linstep" " string" " " - Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 \-3.1") - -.BI "\-accdir" " string" " " - Directions for acceptance linear sampling \- only sign counts! (put in quotes! "\-1 +1 \-1.1") - -.BI "\-radstep" " real" " 0 " - Stepsize (nm/step) for fixed increment radius expansion - .BI "\-[no]restrain" "no " Use the flooding potential with inverted sign \- effects as quasiharmonic restraining potential @@ -281,6 +282,9 @@ You will be prompted for one or more index groups that correspond to the eigenve .BI "\-[no]harmonic" "no " The eigenvalues are interpreted as spring constant +.BI "\-constF" " string" " " + Constant force flooding: manually set the forces for the eigenvectors selected with \-flood (put in quotes! "1.0 2.3 5.1 \-3.1"). No other flooding parameters are needed when specifying the forces directly. + .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/make_ndx.1 b/man/man1/make_ndx.1 index eb856a3ea6..36b0f1cd3b 100644 --- a/man/man1/make_ndx.1 +++ b/man/man1/make_ndx.1 @@ -1,8 +1,8 @@ -.TH make_ndx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME make_ndx - makes index files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3make_ndx\fP .BI "\-f" " conf.gro " @@ -15,13 +15,13 @@ make_ndx - makes index files .SH DESCRIPTION \&Index groups are necessary for almost every gromacs program. \&All these programs can generate default index groups. You ONLY -\&have to use make_ndx when you need SPECIAL index groups. +\&have to use \fB make_ndx\fR when you need SPECIAL index groups. \&There is a default index group for the whole system, 9 default -\&index groups are generated for proteins, a default index group +\&index groups for proteins, and a default index group \&is generated for every other residue name. -\&When no index file is supplied, also make_ndx will generate the +\&When no index file is supplied, also \fB make_ndx\fR will generate the \&default groups. \&With the index editor you can select on atom, residue and chain names \&and numbers. diff --git a/man/man1/mdrun.1 b/man/man1/mdrun.1 index 191bffd54c..d476ec9c2c 100644 --- a/man/man1/mdrun.1 +++ b/man/man1/mdrun.1 @@ -1,8 +1,8 @@ -.TH mdrun 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME mdrun - performs a simulation, do a normal mode analysis or an energy minimization -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3mdrun\fP .BI "\-s" " topol.tpr " @@ -32,6 +32,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " +.BI "\-multidir" " rundir " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " @@ -39,7 +40,6 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati .BI "\-xvg" " enum " .BI "\-[no]pd" "" .BI "\-dd" " vector " -.BI "\-nt" " int " .BI "\-npme" " int " .BI "\-ddorder" " enum " .BI "\-[no]ddcheck" "" @@ -62,20 +62,20 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati .BI "\-reseed" " int " .BI "\-[no]ionize" "" .SH DESCRIPTION -\&The mdrun program is the main computational chemistry engine +\&The \fB mdrun\fR program is the main computational chemistry engine \&within GROMACS. Obviously, it performs Molecular Dynamics simulations, \&but it can also perform Stochastic Dynamics, Energy Minimization, \&test particle insertion or (re)calculation of energies. -\&Normal mode analysis is another option. In this case mdrun +\&Normal mode analysis is another option. In this case \fB mdrun\fR \&builds a Hessian matrix from single conformation. \&For usual Normal Modes\-like calculations, make sure that \&the structure provided is properly energy\-minimized. -\&The generated matrix can be diagonalized by g_nmeig. +\&The generated matrix can be diagonalized by \fB g_nmeig\fR. -\&The mdrun program reads the run input file (\fB \-s\fR) +\&The \fB mdrun\fR program reads the run input file (\fB \-s\fR) \&and distributes the topology over nodes if needed. -\&mdrun produces at least four output files. +\&\fB mdrun\fR produces at least four output files. \&A single log file (\fB \-g\fR) is written, unless the option \&\fB \-seppot\fR is used, in which case each node writes a log file. \&The trajectory file (\fB \-o\fR), contains coordinates, velocities and @@ -92,13 +92,13 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&turned on. -\&When mdrun is started using MPI with more than 1 node, parallelization +\&When \fB mdrun\fR is started using MPI with more than 1 node, parallelization \&is used. By default domain decomposition is used, unless the \fB \-pd\fR \&option is set, which selects particle decomposition. \&With domain decomposition, the spatial decomposition can be set -\&with option \fB \-dd\fR. By default mdrun selects a good decomposition. +\&with option \fB \-dd\fR. By default \fB mdrun\fR selects a good decomposition. \&The user only needs to change this when the system is very inhomogeneous. \&Dynamic load balancing is set with the option \fB \-dlb\fR, \&which can give a significant performance improvement, @@ -119,7 +119,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&this is computationally more efficient starting at about 12 nodes. \&The number of PME nodes is set with option \fB \-npme\fR, \&this can not be more than half of the nodes. -\&By default mdrun makes a guess for the number of PME +\&By default \fB mdrun\fR makes a guess for the number of PME \&nodes when the number of nodes is larger than 11 or performance wise \¬ compatible with the PME grid x dimension. \&But the user should optimize npme. Performance statistics on this issue @@ -133,6 +133,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&This section lists all options that affect the domain decomposition. \& + \&Option \fB \-rdd\fR can be used to set the required maximum distance \&for inter charge\-group bonded interactions. \&Communication for two\-body bonded interactions below the non\-bonded @@ -142,31 +143,34 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&and nearly indepedent of the value of \fB \-rdd\fR. \&With dynamic load balancing option \fB \-rdd\fR also sets \&the lower limit for the domain decomposition cell sizes. -\&By default \fB \-rdd\fR is determined by mdrun based on +\&By default \fB \-rdd\fR is determined by \fB mdrun\fR based on \&the initial coordinates. The chosen value will be a balance \&between interaction range and communication cost. \& + \&When inter charge\-group bonded interactions are beyond -\&the bonded cut\-off distance, mdrun terminates with an error message. +\&the bonded cut\-off distance, \fB mdrun\fR terminates with an error message. \&For pair interactions and tabulated bonds \&that do not generate exclusions, this check can be turned off \&with the option \fB \-noddcheck\fR. \& + \&When constraints are present, option \fB \-rcon\fR influences \&the cell size limit as well. \&Atoms connected by NC constraints, where NC is the LINCS order plus 1, \&should not be beyond the smallest cell size. A error message is \&generated when this happens and the user should change the decomposition \&or decrease the LINCS order and increase the number of LINCS iterations. -\&By default mdrun estimates the minimum cell size required for P\-LINCS +\&By default \fB mdrun\fR estimates the minimum cell size required for P\-LINCS \&in a conservative fashion. For high parallelization it can be useful \&to set the distance required for P\-LINCS with the option \fB \-rcon\fR. \& + \&The \fB \-dds\fR option sets the minimum allowed x, y and/or z scaling -\&of the cells with dynamic load balancing. mdrun will ensure that +\&of the cells with dynamic load balancing. \fB mdrun\fR will ensure that \&the cells can scale down by at least this factor. This option is used \&for the automated spatial decomposition (when not using \fB \-dd\fR) \&as well as for determining the number of grid pulses, which in turn @@ -181,7 +185,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&This can improve performance for highly parallel simulations \&where this global communication step becomes the bottleneck. \&For a global thermostat and/or barostat the temperature -\&and/or pressure will also only be updated every \-gcom steps. +\&and/or pressure will also only be updated every \fB \-gcom\fR steps. \&By default it is set to the minimum of nstcalcenergy and nstlist. @@ -194,19 +198,19 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&ED (essential dynamics) sampling is switched on by using the \fB \-ei\fR \&flag followed by an \fB .edi\fR file. \&The \fB .edi\fR file can be produced using options in the essdyn -\&menu of the WHAT IF program. mdrun produces a \fB .edo\fR file that +\&menu of the WHAT IF program. \fB mdrun\fR produces a \fB .edo\fR file that \&contains projections of positions, velocities and forces onto selected \&eigenvectors. \&When user\-defined potential functions have been selected in the -\&\fB .mdp\fR file the \fB \-table\fR option is used to pass mdrun +\&\fB .mdp\fR file the \fB \-table\fR option is used to pass \fB mdrun\fR \&a formatted table with potential functions. The file is read from -\&either the current directory or from the GMXLIB directory. -\&A number of pre\-formatted tables are presented in the GMXLIB dir, -\&for 6\-8, 6\-9, 6\-10, 6\-11, 6\-12 Lennard Jones potentials with +\&either the current directory or from the \fB GMXLIB\fR directory. +\&A number of pre\-formatted tables are presented in the \fB GMXLIB\fR dir, +\&for 6\-8, 6\-9, 6\-10, 6\-11, 6\-12 Lennard\-Jones potentials with \&normal Coulomb. -\&When pair interactions are present a separate table for pair interaction +\&When pair interactions are present, a separate table for pair interaction \&functions is read using the \fB \-tablep\fR option. @@ -214,7 +218,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&interaction functions are read using the \fB \-tableb\fR option. \&For each different tabulated interaction type the table file name is \&modified in a different way: before the file extension an underscore is -\&appended, then a b for bonds, an a for angles or a d for dihedrals +\&appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals \&and finally the table number of the interaction type. @@ -223,10 +227,16 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&in the \fB .mdp\fR file. -\&With \fB \-multi\fR multiple systems are simulated in parallel. -\&As many input files are required as the number of systems. -\&The system number is appended to the run input and each output filename, -\&for instance topol.tpr becomes topol0.tpr, topol1.tpr etc. +\&With \fB \-multi\fR or \fB \-multidir\fR, multiple systems can be +\&simulated in parallel. +\&As many input files/directories are required as the number of systems. +\&The \fB \-multidir\fR option takes a list of directories (one for each +\&system) and runs in each of them, using the input/output file names, +\&such as specified by e.g. the \fB \-s\fR option, relative to these +\&directories. +\&With \fB \-multi\fR, the system number is appended to the run input +\&and each output filename, for instance \fB topol.tpr\fR becomes +\&\fB topol0.tpr\fR, \fB topol1.tpr\fR etc. \&The number of nodes per system is the total number of nodes \÷d by the number of systems. \&One use of this option is for NMR refinement: when distance @@ -235,8 +245,8 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&With \fB \-replex\fR replica exchange is attempted every given number -\&of steps. The number of replicas is set with the \fB \-multi\fR option, -\&see above. +\&of steps. The number of replicas is set with the \fB \-multi\fR or +\&\fB \-multidir\fR option, described above. \&All run input files should use a different coupling temperature, \&the order of the files is not important. The random seed is set with \&\fB \-reseed\fR. The velocities are scaled and neighbor searching @@ -245,7 +255,7 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&Finally some experimental algorithms can be tested when the \&appropriate options have been given. Currently under -\&investigation are: polarizability, and X\-Ray bombardments. +\&investigation are: polarizability and X\-ray bombardments. \& @@ -267,18 +277,22 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \&A simulation can be continued by reading the full state from file \&with option \fB \-cpi\fR. This option is intelligent in the way that \&if no checkpoint file is found, Gromacs just assumes a normal run and -\&starts from the first step of the tpr file. By default the output +\&starts from the first step of the \fB .tpr\fR file. By default the output \&will be appending to the existing output files. The checkpoint file \&contains checksums of all output files, such that you will never \&loose data when some output files are modified, corrupt or removed. \&There are three scenarios with \fB \-cpi\fR: -\&* no files with matching names are present: new output files are written -\&* all files are present with names and checksums matching those stored +\&\fB *\fR no files with matching names are present: new output files are written + + +\&\fB *\fR all files are present with names and checksums matching those stored \&in the checkpoint file: files are appended -\&* otherwise no files are modified and a fatal error is generated + +\&\fB *\fR otherwise no files are modified and a fatal error is generated + \&With \fB \-noappend\fR new output files are opened and the simulation \&part number is added to all output file names. @@ -309,18 +323,18 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati \& -\&When mdrun receives a TERM signal, it will set nsteps to the current -\&step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is +\&When \fB mdrun\fR receives a TERM signal, it will set nsteps to the current +\&step plus one. When \fB mdrun\fR receives an INT signal (e.g. when ctrl+C is \&pressed), it will stop after the next neighbor search step \&(with nstlist=0 at the next step). \&In both cases all the usual output will be written to file. -\&When running with MPI, a signal to one of the mdrun processes +\&When running with MPI, a signal to one of the \fB mdrun\fR processes \&is sufficient, this signal should not be sent to mpirun or -\&the mdrun process that is the parent of the others. +\&the \fB mdrun\fR process that is the parent of the others. \& -\&When mdrun is started with MPI, it does not run niced by default. +\&When \fB mdrun\fR is started with MPI, it does not run niced by default. .SH FILES .BI "\-s" " topol.tpr" .B Input @@ -430,6 +444,10 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati .B Output, Opt. Index file +.BI "\-multidir" " rundir" +.B Input, Opt., Mult. + Run directory + .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit @@ -452,9 +470,6 @@ mdrun - performs a simulation, do a normal mode analysis or an energy minimizati .BI "\-dd" " vector" " 0 0 0" Domain decomposition grid, 0 is optimize -.BI "\-nt" " int" " 0" - Number of threads to start (0 is guess) - .BI "\-npme" " int" " \-1" Number of separate nodes to be used for PME, \-1 is guess diff --git a/man/man1/mk_angndx.1 b/man/man1/mk_angndx.1 index aad17d3587..2db4099443 100644 --- a/man/man1/mk_angndx.1 +++ b/man/man1/mk_angndx.1 @@ -1,8 +1,8 @@ -.TH mk_angndx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME mk_angndx - generates index files for g_angle -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3mk_angndx\fP .BI "\-s" " topol.tpr " @@ -14,7 +14,7 @@ mk_angndx - generates index files for g_angle .BI "\-[no]hyd" "" .BI "\-hq" " real " .SH DESCRIPTION -\&mk_angndx makes an index file for calculation of +\&\fB mk_angndx\fR makes an index file for calculation of \&angle distributions etc. It uses a run input file (\fB .tpx\fR) for the \&definitions of the angles, dihedrals etc. .SH FILES diff --git a/man/man1/ngmx.1 b/man/man1/ngmx.1 index dfa2e9d87e..118d45726a 100644 --- a/man/man1/ngmx.1 +++ b/man/man1/ngmx.1 @@ -1,8 +1,8 @@ -.TH ngmx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME ngmx - displays a trajectory -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3ngmx\fP .BI "\-f" " traj.xtc " @@ -15,7 +15,7 @@ ngmx - displays a trajectory .BI "\-e" " time " .BI "\-dt" " time " .SH DESCRIPTION -\&ngmx is the Gromacs trajectory viewer. This program reads a +\&\fB ngmx\fR is the GROMACS trajectory viewer. This program reads a \&trajectory file, a run input file and an index file and plots a \&3D structure of your molecule on your standard X Window \&screen. No need for a high end graphics workstation, it even @@ -31,9 +31,8 @@ ngmx - displays a trajectory \&show computational box. -\&Some of the more common X command line options can be used: - -\&\-bg, \-fg change colors, \-font fontname, changes the font. +\&Some of the more common X command line options can be used: +\&\fB \-bg\fR, \fB \-fg\fR change colors, \fB \-font fontname\fR changes the font. .SH FILES .BI "\-f" " traj.xtc" .B Input diff --git a/man/man1/pdb2gmx.1 b/man/man1/pdb2gmx.1 index 6e0e76ddfc..ae103de3af 100644 --- a/man/man1/pdb2gmx.1 +++ b/man/man1/pdb2gmx.1 @@ -1,8 +1,8 @@ -.TH pdb2gmx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME pdb2gmx - converts pdb files to topology and coordinate files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3pdb2gmx\fP .BI "\-f" " eiwit.pdb " @@ -41,22 +41,22 @@ pdb2gmx - converts pdb files to topology and coordinate files .BI "\-[no]renum" "" .BI "\-[no]rtpres" "" .SH DESCRIPTION -\&This program reads a pdb (or gro) file, reads +\&This program reads a \fB .pdb\fR (or \fB .gro\fR) file, reads \&some database files, adds hydrogens to the molecules and generates -\&coordinates in Gromacs (Gromos), or optionally pdb, format -\&and a topology in Gromacs format. +\&coordinates in GROMACS (GROMOS), or optionally \fB .pdb\fR, format +\&and a topology in GROMACS format. \&These files can subsequently be processed to generate a run input file. \& -\&pdb2gmx will search for force fields by looking for +\&\fB pdb2gmx\fR will search for force fields by looking for \&a \fB forcefield.itp\fR file in subdirectories \fB forcefield.ff\fR -\&of the current working directory and of the Gomracs library directory +\&of the current working directory and of the Gromacs library directory \&as inferred from the path of the binary or the \fB GMXLIB\fR environment \&variable. \&By default the forcefield selection is interactive, \&but you can use the \fB \-ff\fR option to specify one of the short names -\&in the list on the command line instead. In that case pdb2gmx just looks +\&in the list on the command line instead. In that case \fB pdb2gmx\fR just looks \&for the corresponding \fB forcefield.ff\fR directory. \& @@ -66,14 +66,14 @@ pdb2gmx - converts pdb files to topology and coordinate files \&If you want to modify or add a residue types, you can copy the force \&field directory from the Gromacs library directory to your current \&working directory. If you want to add new protein residue types, -\&you will need to modify residuetypes.dat in the libary directory +\&you will need to modify \fB residuetypes.dat\fR in the library directory \&or copy the whole library directory to a local directory and set \&the environment variable \fB GMXLIB\fR to the name of that directory. -\&Check chapter 5 of the manual for more information about file formats. +\&Check Chapter 5 of the manual for more information about file formats. \& -\&Note that a pdb file is nothing more than a file format, and it +\&Note that a \fB .pdb\fR file is nothing more than a file format, and it \&need not necessarily contain a protein structure. Every kind of \&molecule for which there is support in the database can be converted. \&If there is no support in the database, you can add it yourself. @@ -89,7 +89,7 @@ pdb2gmx - converts pdb files to topology and coordinate files \&on NE2 or on both. By default these selections are done automatically. \&For His, this is based on an optimal hydrogen bonding \&conformation. Hydrogen bonds are defined based on a simple geometric -\&criterium, specified by the maximum hydrogen\-donor\-acceptor angle +\&criterion, specified by the maximum hydrogen\-donor\-acceptor angle \&and donor\-acceptor distance, which are set by \fB \-angle\fR and \&\fB \-dist\fR respectively. @@ -100,33 +100,33 @@ pdb2gmx - converts pdb files to topology and coordinate files \&if you want a disulfide bridge or distance restraints between \&two protein chains or if you have a HEME group bound to a protein. \&In such cases multiple chains should be contained in a single -\&\fB molecule_type\fR definition. -\&To handle this, pdb2gmx has an option \fB \-chainsep\fR so you can +\&\fB moleculetype\fR definition. +\&To handle this, \fB pdb2gmx\fR has an option \fB \-chainsep\fR so you can \&choose whether a new chain should start when we find a TER record, \&when the chain id changes, combinations of either or both of these \&or fully interactively. -\&pdb2gmx will also check the occupancy field of the pdb file. +\&\fB pdb2gmx\fR will also check the occupancy field of the \fB .pdb\fR file. \&If any of the occupancies are not one, indicating that the atom is \¬ resolved well in the structure, a warning message is issued. -\&When a pdb file does not originate from an X\-Ray structure determination +\&When a \fB .pdb\fR file does not originate from an X\-ray structure determination \&all occupancy fields may be zero. Either way, it is up to the user \&to verify the correctness of the input data (read the article!). -\&During processing the atoms will be reordered according to Gromacs +\&During processing the atoms will be reordered according to GROMACS \&conventions. With \fB \-n\fR an index file can be generated that \&contains one group reordered in the same way. This allows you to -\&convert a Gromos trajectory and coordinate file to Gromos. There is +\&convert a GROMOS trajectory and coordinate file to GROMOS. There is \&one limitation: reordering is done after the hydrogens are stripped \&from the input and before new hydrogens are added. This means that \&you should not use \fB \-ignh\fR. \&The \fB .gro\fR and \fB .g96\fR file formats do not support chain -\&identifiers. Therefore it is useful to enter a pdb file name at -\&the \fB \-o\fR option when you want to convert a multichain pdb file. +\&identifiers. Therefore it is useful to enter a \fB .pdb\fR file name at +\&the \fB \-o\fR option when you want to convert a multi\-chain \fB .pdb\fR file. \& @@ -135,8 +135,8 @@ pdb2gmx - converts pdb files to topology and coordinate files \&hydrogens into virtual sites and fixing angles, which fixes their \&position relative to neighboring atoms. Additionally, all atoms in the \&aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) -\&can be converted into virtual sites, elminating the fast improper dihedral -\&fluctuations in these rings. Note that in this case all other hydrogen +\&can be converted into virtual sites, eliminating the fast improper dihedral +\&fluctuations in these rings. \fB Note\fR that in this case all other hydrogen \&atoms are also converted to virtual sites. The mass of all atoms that are \&converted into virtual sites, is added to the heavy atoms. @@ -185,7 +185,7 @@ pdb2gmx - converts pdb files to topology and coordinate files Condition in PDB files when a new chain and molecule_type should be started: \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR .BI "\-ff" " string" " select" - Force field, interactive by default. Use \-h for information. + Force field, interactive by default. Use \fB \-h\fR for information. .BI "\-water" " enum" " select" Water model to use: \fB select\fR, \fB none\fR, \fB spc\fR, \fB spce\fR, \fB tip3p\fR, \fB tip4p\fR or \fB tip5p\fR @@ -200,22 +200,22 @@ pdb2gmx - converts pdb files to topology and coordinate files Interactive termini selection, iso charged .BI "\-[no]lys" "no " - Interactive Lysine selection, iso charged + Interactive lysine selection, iso charged .BI "\-[no]arg" "no " - Interactive Arganine selection, iso charged + Interactive arginine selection, iso charged .BI "\-[no]asp" "no " - Interactive Aspartic Acid selection, iso charged + Interactive aspartic Acid selection, iso charged .BI "\-[no]glu" "no " - Interactive Glutamic Acid selection, iso charged + Interactive glutamic Acid selection, iso charged .BI "\-[no]gln" "no " - Interactive Glutamine selection, iso neutral + Interactive glutamine selection, iso neutral .BI "\-[no]his" "no " - Interactive Histidine selection, iso checking H\-bonds + Interactive histidine selection, iso checking H\-bonds .BI "\-angle" " real" " 135 " Minimum hydrogen\-donor\-acceptor angle for a H\-bond (degrees) @@ -224,10 +224,10 @@ pdb2gmx - converts pdb files to topology and coordinate files Maximum donor\-acceptor distance for a H\-bond (nm) .BI "\-[no]una" "no " - Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine + Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine .BI "\-[no]ignh" "no " - Ignore hydrogen atoms that are in the pdb file + Ignore hydrogen atoms that are in the coordinate file .BI "\-[no]missing" "no " Continue when atoms are missing, dangerous @@ -248,16 +248,16 @@ pdb2gmx - converts pdb files to topology and coordinate files Change the mass of hydrogens to 2 amu .BI "\-[no]chargegrp" "yes " - Use charge groups in the rtp file + Use charge groups in the \fB .rtp\fR file .BI "\-[no]cmap" "yes " - Use cmap torsions (if enabled in the rtp file) + Use cmap torsions (if enabled in the \fB .rtp\fR file) .BI "\-[no]renum" "no " Renumber the residues consecutively in the output .BI "\-[no]rtpres" "no " - Use rtp entry names as residue names + Use \fB .rtp\fR entry names as residue names .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/tpbconv.1 b/man/man1/tpbconv.1 index 2f0db8ad57..15dcd4dd54 100644 --- a/man/man1/tpbconv.1 +++ b/man/man1/tpbconv.1 @@ -1,8 +1,8 @@ -.TH tpbconv 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME tpbconv - makes a run input file for restarting a crashed run -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3tpbconv\fP .BI "\-s" " topol.tpr " @@ -24,27 +24,31 @@ tpbconv - makes a run input file for restarting a crashed run \&tpbconv can edit run input files in four ways. -\&\fB 1st.\fR by modifying the number of steps in a run input file +\&\fB 1.\fR by modifying the number of steps in a run input file \&with options \fB \-extend\fR, \fB \-until\fR or \fB \-nsteps\fR \&(nsteps=\-1 means unlimited number of steps) -\&\fB 2nd.\fR (OBSOLETE) by creating a run input file +\&\fB 2.\fR (OBSOLETE) by creating a run input file \&for a continuation run when your simulation has crashed due to e.g. \&a full disk, or by making a continuation run input file. \&This option is obsolete, since mdrun now writes and reads \&checkpoint files. -\&Note that a frame with coordinates and velocities is needed. +\&\fB Note\fR that a frame with coordinates and velocities is needed. \&When pressure and/or Nose\-Hoover temperature coupling is used \&an energy file can be supplied to get an exact continuation \&of the original run. -\&\fB 3rd.\fR by creating a tpx file for a subset of your original +\&\fB 3.\fR by creating a \fB .tpx\fR file for a subset of your original \&tpx file, which is useful when you want to remove the solvent from -\&your tpx file, or when you want to make e.g. a pure Ca tpx file. -\&\fB WARNING: this tpx file is not fully functional\fR. -\&\fB 4th.\fR by setting the charges of a specified group +\&your \fB .tpx\fR file, or when you want to make e.g. a pure C[GRK]alpha[grk] \fB .tpx\fR file. +\&Note that you may need to use \fB \-nsteps \-1\fR (or similar) to get +\&this to work. +\&\fB WARNING: this \fB .tpx\fR file is not fully functional\fR. + + +\&\fB 4.\fR by setting the charges of a specified group \&to zero. This is useful when doing free energy estimates \&using the LIE (Linear Interaction Energy) method. .SH FILES diff --git a/man/man1/trjcat.1 b/man/man1/trjcat.1 index 56ab69a999..55cb9694b5 100644 --- a/man/man1/trjcat.1 +++ b/man/man1/trjcat.1 @@ -1,8 +1,8 @@ -.TH trjcat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME trjcat - concatenates trajectory files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3trjcat\fP .BI "\-f" " traj.xtc " @@ -25,12 +25,12 @@ trjcat - concatenates trajectory files .BI "\-[no]overwrite" "" .BI "\-[no]cat" "" .SH DESCRIPTION -\&trjcat concatenates several input trajectory files in sorted order. +\&\fB trjcat\fR concatenates several input trajectory files in sorted order. \&In case of double time frames the one in the later file is used. \&By specifying \fB \-settime\fR you will be asked for the start time \&of each file. The input files are taken from the command line, -\&such that a command like \fB trjcat \-o fixed.trr *.trr\fR should do -\&the trick. Using \fB \-cat\fR you can simply paste several files +\&such that a command like \fB trjcat \-f *.trr \-o fixed.trr\fR should do +\&the trick. Using \fB \-cat\fR, you can simply paste several files \&together without removal of frames with identical time stamps. @@ -42,19 +42,19 @@ trjcat - concatenates trajectory files \&If the \fB \-demux\fR option is given, the N trajectories that are -\&read, are written in another order as specified in the xvg file. -\&The xvg file should contain something like: +\&read, are written in another order as specified in the \fB .xvg\fR file. +\&The \fB .xvg\fR file should contain something like: -\&0 0 1 2 3 4 5 +\&\fB 0 0 1 2 3 4 5 -\&2 1 0 2 3 5 4 +\&2 1 0 2 3 5 4\fR \&Where the first number is the time, and subsequent numbers point to \&trajectory indices. \&The frames corresponding to the numbers present at the first line \&are collected into the output trajectory. If the number of frames in -\&the trajectory does not match that in the xvg file then the program +\&the trajectory does not match that in the \fB .xvg\fR file then the program \&tries to be smart. Beware. .SH FILES .BI "\-f" " traj.xtc" @@ -99,7 +99,7 @@ trjcat - concatenates trajectory files Only write frame when t MOD dt = first time (ps) .BI "\-prec" " int" " 3" - Precision for .xtc and .gro writing in number of decimal places + Precision for \fB .xtc\fR and \fB .gro\fR writing in number of decimal places .BI "\-[no]vel" "yes " Read and write velocities if possible @@ -111,13 +111,13 @@ trjcat - concatenates trajectory files Sort trajectory files (not frames) .BI "\-[no]keeplast" "no " - keep overlapping frames at end of trajectory + Keep overlapping frames at end of trajectory .BI "\-[no]overwrite" "no " - overwrite overlapping frames during appending + Overwrite overlapping frames during appending .BI "\-[no]cat" "no " - do not discard double time frames + Do not discard double time frames .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/trjconv.1 b/man/man1/trjconv.1 index fbb082ea55..37d9729f0a 100644 --- a/man/man1/trjconv.1 +++ b/man/man1/trjconv.1 @@ -1,8 +1,8 @@ -.TH trjconv 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME trjconv - converts and manipulates trajectory files -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3trjconv\fP .BI "\-f" " traj.xtc " @@ -31,6 +31,7 @@ trjconv - converts and manipulates trajectory files .BI "\-[no]center" "" .BI "\-boxcenter" " enum " .BI "\-box" " vector " +.BI "\-clustercenter" " vector " .BI "\-trans" " vector " .BI "\-shift" " vector " .BI "\-fit" " enum " @@ -47,7 +48,7 @@ trjconv - converts and manipulates trajectory files .BI "\-dropover" " real " .BI "\-[no]conect" "" .SH DESCRIPTION -\&trjconv can convert trajectory files in many ways: +\&\fB trjconv\fR can convert trajectory files in many ways: \&\fB 1.\fR from one format to another @@ -68,7 +69,7 @@ trjconv - converts and manipulates trajectory files \&\fB 9.\fR cut the trajectory in small subtrajectories according \&to information in an index file. This allows subsequent analysis of -\&the subtrajectories that could, for example be the result of a +\&the subtrajectories that could, for example, be the result of a \&cluster analysis. Use option \fB \-sub\fR. \&This assumes that the entries in the index file are frame numbers and \&dumps each group in the index file to a separate trajectory file. @@ -77,7 +78,7 @@ trjconv - converts and manipulates trajectory files \&in an \fB .xvg\fR file. -\&The program \fB trjcat\fR can concatenate multiple trajectory files. +\&The program \fB trjcat\fR is better suited for concatenating multiple trajectory files. \& @@ -91,7 +92,7 @@ trjconv - converts and manipulates trajectory files \&is always taken from \fB \-ndec\fR, when this option is set. \&All other formats have fixed precision. \fB .trr\fR and \fB .trj\fR \&output can be single or double precision, depending on the precision -\&of the trjconv binary. +\&of the \fB trjconv\fR binary. \&Note that velocities are only supported in \&\fB .trr\fR, \fB .trj\fR, \fB .gro\fR and \fB .g96\fR files. @@ -103,7 +104,7 @@ trjconv - converts and manipulates trajectory files \&Option \fB \-sep\fR can be used to write every frame to a separate -\&.gro, .g96 or .pdb file, default all frames all written to one file. +\&\fB .gro, .g96\fR or \fB .pdb\fR file. By default, all frames all written to one file. \&\fB .pdb\fR files with all frames concatenated can be viewed with \&\fB rasmol \-nmrpdb\fR. @@ -117,9 +118,9 @@ trjconv - converts and manipulates trajectory files \&There are two options for fitting the trajectory to a reference -\&either for essential dynamics analysis or for whatever. +\&either for essential dynamics analysis, etc. \&The first option is just plain fitting to a reference structure -\&in the structure file, the second option is a progressive fit +\&in the structure file. The second option is a progressive fit \&in which the first timeframe is fitted to the reference structure \&in the structure file to obtain and each subsequent timeframe is \&fitted to the previously fitted structure. This way a continuous @@ -131,28 +132,32 @@ trjconv - converts and manipulates trajectory files \&Option \fB \-pbc\fR sets the type of periodic boundary condition \&treatment: -\&* \fB mol\fR puts the center of mass of molecules in the box. +\&\fB * mol\fR puts the center of mass of molecules in the box. -\&* \fB res\fR puts the center of mass of residues in the box. +\&\fB * res\fR puts the center of mass of residues in the box. -\&* \fB atom\fR puts all the atoms in the box. +\&\fB * atom\fR puts all the atoms in the box. -\&* \fB nojump\fR checks if atoms jump across the box and then puts +\&\fB * nojump\fR checks if atoms jump across the box and then puts \&them back. This has the effect that all molecules \&will remain whole (provided they were whole in the initial -\&conformation), note that this ensures a continuous trajectory but +\&conformation). \fB Note\fR that this ensures a continuous trajectory but \&molecules may diffuse out of the box. The starting configuration \&for this procedure is taken from the structure file, if one is \&supplied, otherwise it is the first frame. -\&* \fB cluster\fR clusters all the atoms in the selected index -\&such that they are all closest to the center of mass of the cluster -\&which is iteratively updated. Note that this will only give meaningful +\&\fB * cluster\fR clusters all the atoms in the selected index +\&such that they are all closest to the center of mass of the cluster, +\&which is iteratively updated. \fB Note\fR that this will only give meaningful \&results if you in fact have a cluster. Luckily that can be checked \&afterwards using a trajectory viewer. Note also that if your molecules \&are broken this will not work either. -\&* \fB whole\fR only makes broken molecules whole. +\&The separate option \fB \-clustercenter\fR can be used to specify an +\&approximate center for the cluster. This is useful e.g. if you have +\&two big vesicles, and you want to maintain their relative positions. + +\&\fB * whole\fR only makes broken molecules whole. \&Option \fB \-ur\fR sets the unit cell representation for options @@ -163,7 +168,7 @@ trjconv - converts and manipulates trajectory files \&\fB tric\fR is the triclinic unit cell. \&\fB compact\fR puts all atoms at the closest distance from the center \&of the box. This can be useful for visualizing e.g. truncated -\&octahedrons. The center for options \fB tric\fR and \fB compact\fR +\&octahedra. The center for options \fB tric\fR and \fB compact\fR \&is \fB tric\fR (see below), unless the option \fB \-boxcenter\fR \&is set differently. @@ -179,22 +184,19 @@ trjconv - converts and manipulates trajectory files \&want all molecules in the box after the centering. -\&With \fB \-dt\fR it is possible to reduce the number of +\&With \fB \-dt\fR, it is possible to reduce the number of \&frames in the output. This option relies on the accuracy of the times \&in your input trajectory, so if these are inaccurate use the \&\fB \-timestep\fR option to modify the time (this can be done -\&simultaneously). For making smooth movies the program \fB g_filter\fR +\&simultaneously). For making smooth movies, the program \fB g_filter\fR \&can reduce the number of frames while using low\-pass frequency \&filtering, this reduces aliasing of high frequency motions. -\&Using \fB \-trunc\fR trjconv can truncate \fB .trj\fR in place, i.e. +\&Using \fB \-trunc\fR \fB trjconv\fR can truncate \fB .trj\fR in place, i.e. \&without copying the file. This is useful when a run has crashed -\&during disk I/O (one more disk full), or when two contiguous -\&trajectories must be concatenated without have double frames. - - -\&\fB trjcat\fR is more suitable for concatenating trajectory files. +\&during disk I/O (i.e. full disk), or when two contiguous +\&trajectories must be concatenated without having double frames. \&Option \fB \-dump\fR can be used to extract a frame at or near @@ -254,7 +256,7 @@ trjconv - converts and manipulates trajectory files Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR @@ -292,6 +294,9 @@ trjconv - converts and manipulates trajectory files .BI "\-box" " vector" " 0 0 0" Size for new cubic box (default: read from input) +.BI "\-clustercenter" " vector" " 0 0 0" + Optional starting point for pbc cluster option + .BI "\-trans" " vector" " 0 0 0" All coordinates will be translated by trans. This can advantageously be combined with \-pbc mol \-ur compact. @@ -311,7 +316,7 @@ trjconv - converts and manipulates trajectory files Read and write forces if possible .BI "\-trunc" " time" " \-1 " - Truncate input trj file after this time (ps) + Truncate input trajectory file after this time (ps) .BI "\-exec" " string" " " Execute command for every output frame with the frame number as argument @@ -326,7 +331,7 @@ trjconv - converts and manipulates trajectory files Write each frame to a separate .gro, .g96 or .pdb file .BI "\-nzero" " int" " 0" - Prepend file number in case you use the \-sep flag with this number of zeroes + If the \-sep flag is set, use these many digits for the file numbers and prepend zeros as needed .BI "\-dropunder" " real" " 0 " Drop all frames below this value @@ -335,7 +340,7 @@ trjconv - converts and manipulates trajectory files Drop all frames above this value .BI "\-[no]conect" "no " - Add conect records when writing pdb files. Useful for visualization of non\-standard molecules, e.g. coarse grained ones + Add conect records when writing \fB .pdb\fR files. Useful for visualization of non\-standard molecules, e.g. coarse grained ones .SH SEE ALSO .BR gromacs(7) diff --git a/man/man1/trjorder.1 b/man/man1/trjorder.1 index c8827065b2..d8c75c00e6 100644 --- a/man/man1/trjorder.1 +++ b/man/man1/trjorder.1 @@ -1,8 +1,8 @@ -.TH trjorder 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME trjorder - orders molecules according to their distance to a group -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3trjorder\fP .BI "\-f" " traj.xtc " @@ -23,7 +23,7 @@ trjorder - orders molecules according to their distance to a group .BI "\-r" " real " .BI "\-[no]z" "" .SH DESCRIPTION -\&trjorder orders molecules according to the smallest distance +\&\fB trjorder\fR orders molecules according to the smallest distance \&to atoms in a reference group \&or on z\-coordinate (with option \fB \-z\fR). \&With distance ordering, it will ask for a group of reference @@ -36,7 +36,7 @@ trjorder - orders molecules according to their distance to a group \&to the output trajectory. -\&trjorder can be useful for e.g. analyzing the n waters closest to a +\&\fB trjorder\fR can be useful for e.g. analyzing the n waters closest to a \&protein. \&In that case the reference group would be the protein and the group \&of molecules would consist of all the water atoms. When an index group @@ -45,8 +45,8 @@ trjorder - orders molecules according to their distance to a group \& -\&If the output file is a pdb file, the distance to the reference target -\&will be stored in the B\-factor field in order to color with e.g. rasmol. +\&If the output file is a \fB .pdb\fR file, the distance to the reference target +\&will be stored in the B\-factor field in order to color with e.g. Rasmol. \& diff --git a/man/man1/xpm2ps.1 b/man/man1/xpm2ps.1 index 4b4684403f..277efb3c2b 100644 --- a/man/man1/xpm2ps.1 +++ b/man/man1/xpm2ps.1 @@ -1,8 +1,8 @@ -.TH xpm2ps 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" +.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" .SH NAME xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) -.B VERSION 4.5 +.B VERSION 4.5.4-dev-20110404-3c0e5ec .SH SYNOPSIS \f3xpm2ps\fP .BI "\-f" " root.xpm " @@ -32,30 +32,30 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) .BI "\-cmin" " real " .BI "\-cmax" " real " .SH DESCRIPTION -\&xpm2ps makes a beautiful color plot of an XPixelMap file. +\&\fB xpm2ps\fR makes a beautiful color plot of an XPixelMap file. \&Labels and axis can be displayed, when they are supplied \&in the correct matrix format. -\&Matrix data may be generated by programs such as do_dssp, g_rms or -\&g_mdmat. +\&Matrix data may be generated by programs such as \fB do_dssp\fR, \fB g_rms\fR or +\&\fB g_mdmat\fR. -\&Parameters are set in the \fB m2p\fR file optionally supplied with -\&\fB \-di\fR. Reasonable defaults are provided. Settings for the y\-axis -\&default to those for the x\-axis. Font names have a defaulting hierarchy: +\&Parameters are set in the \fB .m2p\fR file optionally supplied with +\&\fB \-di\fR. Reasonable defaults are provided. Settings for the \fI y\fR\-axis +\&default to those for the \fI x\fR\-axis. Font names have a defaulting hierarchy: \&titlefont \- legendfont; titlefont \- (xfont \- yfont \- ytickfont) \&\- xtickfont, e.g. setting titlefont sets all fonts, setting xfont \&sets yfont, ytickfont and xtickfont. -\&When no \fB m2p\fR file is supplied, many setting are set by -\&command line options. The most important option is \fB \-size\fR +\&When no \fB .m2p\fR file is supplied, many settings are taken from +\&command line options. The most important option is \fB \-size\fR, \&which sets the size of the whole matrix in postscript units. \&This option can be overridden with the \fB \-bx\fR and \fB \-by\fR -\&options (and the corresponding parameters in the \fB m2p\fR file), +\&options (and the corresponding parameters in the \fB .m2p\fR file), \&which set the size of a single matrix element. -\&With \fB \-f2\fR a 2nd matrix file can be supplied, both matrix +\&With \fB \-f2\fR a second matrix file can be supplied. Both matrix \&files will be read simultaneously and the upper left half of the \&first one (\fB \-f\fR) is plotted together with the lower right \&half of the second one (\fB \-f2\fR). The diagonal will contain @@ -67,7 +67,7 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) \&If the color coding and legend labels of both matrices are identical, \&only one legend will be displayed, else two separate legends are \&displayed. -\&With \fB \-combine\fR an alternative operation can be selected +\&With \fB \-combine\fR, an alternative operation can be selected \&to combine the matrices. The output range is automatically set \&to the actual range of the combined matrix. This can be overridden \&with \fB \-cmin\fR and \fB \-cmax\fR. @@ -75,10 +75,10 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) \&\fB \-title\fR can be set to \fB none\fR to suppress the title, or to \&\fB ylabel\fR to show the title in the Y\-label position (alongside -\&the Y\-axis). +\&the \fI y\fR\-axis). -\&With the \fB \-rainbow\fR option dull grey\-scale matrices can be turned +\&With the \fB \-rainbow\fR option, dull grayscale matrices can be turned \&into attractive color pictures. @@ -120,7 +120,7 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) Set the nicelevel .BI "\-[no]w" "no " - View output xvg, xpm, eps and pdb files + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-[no]frame" "yes " Display frame, ticks, labels, title and legend @@ -141,7 +141,7 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) Horizontal size of the matrix in ps units .BI "\-bx" " real" " 0 " - Element x\-size, overrides \-size (also y\-size when \-by is not set) + Element x\-size, overrides \fB \-size\fR (also y\-size when \fB \-by\fR is not set) .BI "\-by" " real" " 0 " Element y\-size @@ -156,10 +156,10 @@ xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) only write out every nr\-th row and column .BI "\-[no]zeroline" "no " - insert line in xpm matrix where axis label is zero + insert line in \fB .xpm\fR matrix where axis label is zero .BI "\-legoffset" " int" " 0" - Skip first N colors from xpm file for the legend + Skip first N colors from \fB .xpm\fR file for the legend .BI "\-combine" " enum" " halves" Combine two matrices: \fB halves\fR, \fB add\fR, \fB sub\fR, \fB mult\fR or \fB div\fR diff --git a/share/html/online/Makefile.am b/share/html/online/Makefile.am index 8e0bcffd89..37d5fc55d7 100644 --- a/share/html/online/Makefile.am +++ b/share/html/online/Makefile.am @@ -35,7 +35,7 @@ online_DATA = \ g_dielectric.html g_saltbr.html mdrun.html xrama.html \ g_dih.html g_sas.html mk_angndx.html xtc.html \ g_dipoles.html g_sgangle.html mtx.html xvg.html \ - g_densmap.html g_sham.html make_edi.html \ + g_densmap.html g_sham.html make_edi.html g_densorder.html \ style.css \ water.html gmxdemo.html speptide.html yourown.html \ methanol.html mixed.html protunf.html diff --git a/share/html/online/g_densorder.html b/share/html/online/g_densorder.html new file mode 100644 index 0000000000..6df73d52dd --- /dev/null +++ b/share/html/online/g_densorder.html @@ -0,0 +1,63 @@ + + +g_densorder + + + +
+ + + +
+

g_densorder

Main Table of Contents

VERSION 4.5.4-dev-20110404-3c0e5ec
+Mon 4 Apr 2011

+
+

Description

+

+A small program to reduce a two-phase density distribution +along an axis, computed over a MD trajectory +to 2D surfaces fluctuating in time, by a fit to +a functional profile for interfacial densities +A time-averaged spatial representation of the +interfaces can be output with the option -tavg +

+

Files

+ + + + + + + + + +
optionfilenametypedescription
-s topol.tpr Input Run input file: tpr tpb tpa
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input Index file
-o Density4D.dat Output, Opt. Generic data file
-or hello.out Output, Opt., Mult. Generic output file
-og interface.xpm Output, Opt., Mult. X PixMap compatible matrix file
-Spect intfspect.out Output, Opt., Mult. Generic output file
+

+

Other options

+ + + + + + + + + + + + + + + + + + + +
optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]1d bool no Pseudo-1d interface geometry
-bw real 0.2 Binwidth of density distribution tangential to interface
-bwn real 0.05 Binwidth of density distribution normal to interface
-order int 0 Order of Gaussian filter, order 0 equates to NO filtering
-axis string Z Axis Direction - X, Y or Z
-method enum bisect Interface location method: bisect or functional
-d1 real 0 Bulk density phase 1 (at small z)
-d2 real 1000 Bulk density phase 2 (at large z)
-tblock int 100 Number of frames in one time-block average
-nlevel int 100 Number of Height levels in 2D - XPixMaps
+

+

+
+http://www.gromacs.org
+gromacs@gromacs.org
+
+ -- 2.11.4.GIT