From 7ef854756befad6d50d778fb31d8953fc450a562 Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Mon, 4 Apr 2011 14:31:56 +0200 Subject: [PATCH] New entry --- man/man1/do_dssp.1 | 4 +- man/man1/editconf.1 | 4 +- man/man1/eneconv.1 | 4 +- man/man1/g_anadock.1 | 4 +- man/man1/g_anaeig.1 | 4 +- man/man1/g_analyze.1 | 20 ++++---- man/man1/g_angle.1 | 4 +- man/man1/g_bar.1 | 32 ++++++------ man/man1/g_bond.1 | 4 +- man/man1/g_bundle.1 | 4 +- man/man1/g_chi.1 | 36 +++++++------- man/man1/g_cluster.1 | 4 +- man/man1/g_clustsize.1 | 4 +- man/man1/g_confrms.1 | 4 +- man/man1/g_covar.1 | 4 +- man/man1/g_current.1 | 4 +- man/man1/g_density.1 | 4 +- man/man1/g_densmap.1 | 4 +- man/man1/g_densorder.1 | 123 +++++++++++++++++++++++++++++++++++++++++++++++ man/man1/g_dielectric.1 | 12 ++--- man/man1/g_dih.1 | 4 +- man/man1/g_dipoles.1 | 8 +-- man/man1/g_disre.1 | 4 +- man/man1/g_dist.1 | 4 +- man/man1/g_dyndom.1 | 4 +- man/man1/g_enemat.1 | 4 +- man/man1/g_energy.1 | 12 ++--- man/man1/g_filter.1 | 6 +-- man/man1/g_gyrate.1 | 4 +- man/man1/g_h2order.1 | 4 +- man/man1/g_hbond.1 | 6 +-- man/man1/g_helix.1 | 18 +++---- man/man1/g_helixorient.1 | 14 +++--- man/man1/g_lie.1 | 4 +- man/man1/g_mdmat.1 | 4 +- man/man1/g_membed.1 | 4 +- man/man1/g_mindist.1 | 4 +- man/man1/g_morph.1 | 4 +- man/man1/g_msd.1 | 4 +- man/man1/g_nmeig.1 | 4 +- man/man1/g_nmens.1 | 4 +- man/man1/g_nmtraj.1 | 4 +- man/man1/g_order.1 | 4 +- man/man1/g_polystat.1 | 4 +- man/man1/g_potential.1 | 4 +- man/man1/g_principal.1 | 4 +- man/man1/g_protonate.1 | 4 +- man/man1/g_rama.1 | 6 +-- man/man1/g_rdf.1 | 4 +- man/man1/g_rms.1 | 8 +-- man/man1/g_rmsdist.1 | 4 +- man/man1/g_rmsf.1 | 4 +- man/man1/g_rotacf.1 | 4 +- man/man1/g_rotmat.1 | 4 +- man/man1/g_saltbr.1 | 4 +- man/man1/g_sas.1 | 4 +- man/man1/g_select.1 | 4 +- man/man1/g_sgangle.1 | 4 +- man/man1/g_sham.1 | 4 +- man/man1/g_sigeps.1 | 6 +-- man/man1/g_sorient.1 | 16 +++--- man/man1/g_spatial.1 | 4 +- man/man1/g_spol.1 | 4 +- man/man1/g_tcaf.1 | 16 +++--- man/man1/g_traj.1 | 4 +- man/man1/g_tune_pme.1 | 4 +- man/man1/g_vanhove.1 | 4 +- man/man1/g_velacc.1 | 4 +- man/man1/g_wham.1 | 12 ++--- man/man1/g_wheel.1 | 4 +- man/man1/g_x2top.1 | 4 +- man/man1/g_xrama.1 | 4 +- man/man1/genbox.1 | 4 +- man/man1/genconf.1 | 4 +- man/man1/genion.1 | 4 +- man/man1/genrestr.1 | 6 +-- man/man1/gmxcheck.1 | 4 +- man/man1/gmxdump.1 | 4 +- man/man1/grompp.1 | 4 +- man/man1/make_edi.1 | 12 ++--- man/man1/make_ndx.1 | 4 +- man/man1/mdrun.1 | 4 +- man/man1/mk_angndx.1 | 4 +- man/man1/ngmx.1 | 4 +- man/man1/pdb2gmx.1 | 4 +- man/man1/tpbconv.1 | 6 +-- man/man1/trjcat.1 | 4 +- man/man1/trjconv.1 | 4 +- man/man1/trjorder.1 | 4 +- man/man1/xpm2ps.1 | 4 +- 90 files changed, 389 insertions(+), 266 deletions(-) create mode 100644 man/man1/g_densorder.1 diff --git a/man/man1/do_dssp.1 b/man/man1/do_dssp.1 index 12556d9244..8d7f0d35c4 100644 --- a/man/man1/do_dssp.1 +++ b/man/man1/do_dssp.1 @@ -1,8 +1,8 @@ -.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME do_dssp - assigns secondary structure and calculates solvent accessible surface area -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3do_dssp\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/editconf.1 b/man/man1/editconf.1 index 60126515c4..880688448c 100644 --- a/man/man1/editconf.1 +++ b/man/man1/editconf.1 @@ -1,8 +1,8 @@ -.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME editconf - edits the box and writes subgroups -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3editconf\fP .BI "\-f" " conf.gro " diff --git a/man/man1/eneconv.1 b/man/man1/eneconv.1 index 631f7213ae..703abceda7 100644 --- a/man/man1/eneconv.1 +++ b/man/man1/eneconv.1 @@ -1,8 +1,8 @@ -.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME eneconv - converts energy files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3eneconv\fP .BI "\-f" " ener.edr " diff --git a/man/man1/g_anadock.1 b/man/man1/g_anadock.1 index 9d14067403..fc8b6c2b16 100644 --- a/man/man1/g_anadock.1 +++ b/man/man1/g_anadock.1 @@ -1,8 +1,8 @@ -.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_anadock - cluster structures from Autodock runs -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_anadock\fP .BI "\-f" " eiwit.pdb " diff --git a/man/man1/g_anaeig.1 b/man/man1/g_anaeig.1 index febbb0393b..b23c3d0b56 100644 --- a/man/man1/g_anaeig.1 +++ b/man/man1/g_anaeig.1 @@ -1,8 +1,8 @@ -.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_anaeig - analyzes the eigenvectors -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_anaeig\fP .BI "\-v" " eigenvec.trr " diff --git a/man/man1/g_analyze.1 b/man/man1/g_analyze.1 index 2ff3a3b248..7237823be8 100644 --- a/man/man1/g_analyze.1 +++ b/man/man1/g_analyze.1 @@ -1,8 +1,8 @@ -.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_analyze - analyzes data sets -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_analyze\fP .BI "\-f" " graph.xvg " @@ -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 [GRK]pi[grk] t) dt)2 / int0\-T y(t) y(t) dt +2 (int0\-T y(t) cos(i pi 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) = [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)) + +\&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) + -\& (1\-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(\-t/[GRK]tau[grk]2) \- 1) [GRK]tau[grk]2/t + 1)))), +\& (1\-alpha) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))), where T is the total time. -\&[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f2(t) to error2. +\&alpha, tau1 and tau2 are obtained by fitting f2(t) to error2. \&When the actual block average is very close to the analytical curve, -\&the error is [GRK]sigma[grk]\fB *\fRsqrt(2/T (a [GRK]tau[grk]1 + (1\-a) [GRK]tau[grk]2)). +\&the error is sigma\fB *\fRsqrt(2/T (a tau1 + (1\-a) tau2)). \&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([GRK]pi[grk] t/len) where t goes from \-len/2 +\&The filter is proportional to cos(pi 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. @@ -234,7 +234,7 @@ 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 \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. + 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 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. .BI "\-[no]luzar" "no " 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). @@ -249,7 +249,7 @@ Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis 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/[GRK]tau[grk]) + If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau) .BI "\-filter" " real" " 0 " Print the high\-frequency fluctuation after filtering with a cosine filter of length diff --git a/man/man1/g_angle.1 b/man/man1/g_angle.1 index 272c893bd8..be7c954eb3 100644 --- a/man/man1/g_angle.1 +++ b/man/man1/g_angle.1 @@ -1,8 +1,8 @@ -.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_angle - calculates distributions and correlations for angles and dihedrals -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_angle\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_bar.1 b/man/man1/g_bar.1 index 824d5af1b6..3ecfe5b09e 100644 --- a/man/man1/g_bar.1 +++ b/man/man1/g_bar.1 @@ -1,8 +1,8 @@ -.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_bar - calculates free energy difference estimates through Bennett's acceptance ratio -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_bar\fP .BI "\-f" " dhdl.xvg " @@ -31,12 +31,12 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance \&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 +\&controlled by a parameter, lambda (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] +\&vice versa. If the Hamiltonian does not depend linearly on lambda \&(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), +\&with respect to lambda, 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. @@ -46,20 +46,20 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance \&Two types of input files are supported: \&\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 +\& that the \fI y\fR\-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 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. +\& with dH/dlambda and Deltalambda. The lambda values are inferred +\& from the legends: lambda of the simulation from the legend of dH/dlambda +\& and the foreign lambda values from the legends of Delta H. -\&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 +\&The lambda of the simulation is parsed from \fB dhdl.xvg\fR file's legend +\&containing the string 'dH', the foreign lambda values from the legend \&containing the capitalized letters 'D' and 'H'. The temperature \&is parsed from the legend line containing 'T ='. @@ -68,7 +68,7 @@ g_bar - calculates free energy difference estimates through Bennett's acceptance \&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 temperature and lambda values are automatically deduced from \&the \fB ener.edr\fR file. The free energy estimates are determined using BAR with bisection, @@ -83,7 +83,7 @@ The free energy estimates are determined using BAR with bisection, \&\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 +\&lambda 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 @@ -97,9 +97,9 @@ The free energy estimates are determined using BAR with bisection, \&kT (together with their computed error estimate). The printed \&values are: -\&\fB *\fR lam_A: the [GRK]lambda[grk] values for point A. +\&\fB *\fR lam_A: the lambda values for point A. -\&\fB *\fR lam_B: the [GRK]lambda[grk] values for point B. +\&\fB *\fR lam_B: the lambda values for point B. \&\fB *\fR DG: the free energy estimate. diff --git a/man/man1/g_bond.1 b/man/man1/g_bond.1 index 44c354d488..8944075977 100644 --- a/man/man1/g_bond.1 +++ b/man/man1/g_bond.1 @@ -1,8 +1,8 @@ -.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_bond - calculates distances between atoms -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_bond\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_bundle.1 b/man/man1/g_bundle.1 index 72b0f6a23e..a80d361c97 100644 --- a/man/man1/g_bundle.1 +++ b/man/man1/g_bundle.1 @@ -1,8 +1,8 @@ -.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_bundle - analyzes bundles of axes, e.g. helices -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_bundle\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_chi.1 b/man/man1/g_chi.1 index c4d6b17232..5625ba215e 100644 --- a/man/man1/g_chi.1 +++ b/man/man1/g_chi.1 @@ -1,8 +1,8 @@ -.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_chi - calculates everything you want to know about chi and other dihedrals -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_chi\fP .BI "\-s" " conf.gro " @@ -52,7 +52,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION -\&\fB g_chi\fR computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your +\&\fB g_chi\fR computes phi, psi, omega, and chi dihedrals for all your \&amino acid backbone and sidechains. \&It can compute dihedral angle as a function of time, and as \&histogram distributions. @@ -61,7 +61,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals \&If option \fB \-corr\fR is given, the program will \&calculate dihedral autocorrelation functions. The function used -\&is C(t) = cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) . The use of cosines +\&is C(t) = cos(chi(tau)) cos(chi(tau+t)) . The use of cosines \&rather than angles themselves, resolves the problem of periodicity. \&(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032\-2041). \&Separate files for each dihedral of each residue @@ -86,9 +86,9 @@ 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 [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 +\&All rotamers are taken as 3\-fold, except for omega 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 \&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 @@ -103,7 +103,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals \&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 +\&1+9(chi1\-1)+3(chi2\-1)+(chi3\-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 @@ -114,9 +114,9 @@ g_chi - calculates everything you want to know about chi and other dihedrals \&and their occupancies to \fB histo\-chiproduct(RESIDUE)(nresnr).xvg\fR. -\&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. +\&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. .SH FILES .BI "\-s" " conf.gro" .B Input @@ -195,16 +195,16 @@ g_chi - calculates everything you want to know about chi and other dihedrals starting residue .BI "\-[no]phi" "no " - Output for [GRK]phi[grk] dihedral angles + Output for phi dihedral angles .BI "\-[no]psi" "no " - Output for [GRK]psi[grk] dihedral angles + Output for psi dihedral angles .BI "\-[no]omega" "no " - Output for [GRK]omega[grk] dihedrals (peptide bonds) + Output for omega dihedrals (peptide bonds) .BI "\-[no]rama" "no " - Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots + Generate phi/psi and chi1/chi2 Ramachandran plots .BI "\-[no]viol" "no " Write a file that gives 0 or 1 for violated Ramachandran angles @@ -219,7 +219,7 @@ 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 [GRK]phi[grk]/[GRK]psi[grk] angles + Compute chemical shifts from phi/psi angles .BI "\-binwidth" " int" " 1" bin width for histograms (degrees) @@ -228,7 +228,7 @@ g_chi - calculates everything you want to know about chi and other dihedrals 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 [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 + 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 .BI "\-[no]normhisto" "yes " Normalize histograms @@ -272,7 +272,7 @@ 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. -\- [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. +\- 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 \fB g_rama\fR. \- \fB \-r0\fR option does not work properly diff --git a/man/man1/g_cluster.1 b/man/man1/g_cluster.1 index cda3f76ba5..774aa6d149 100644 --- a/man/man1/g_cluster.1 +++ b/man/man1/g_cluster.1 @@ -1,8 +1,8 @@ -.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_cluster - clusters structures -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_cluster\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_clustsize.1 b/man/man1/g_clustsize.1 index a78bcc07a8..ddbfcf4843 100644 --- a/man/man1/g_clustsize.1 +++ b/man/man1/g_clustsize.1 @@ -1,8 +1,8 @@ -.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_clustsize - calculate size distributions of atomic clusters -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_clustsize\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_confrms.1 b/man/man1/g_confrms.1 index 6f99dffb23..af439a0dc1 100644 --- a/man/man1/g_confrms.1 +++ b/man/man1/g_confrms.1 @@ -1,8 +1,8 @@ -.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_confrms - fits two structures and calculates the rmsd -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_confrms\fP .BI "\-f1" " conf1.gro " diff --git a/man/man1/g_covar.1 b/man/man1/g_covar.1 index 9793b8157b..4d90b2bd82 100644 --- a/man/man1/g_covar.1 +++ b/man/man1/g_covar.1 @@ -1,8 +1,8 @@ -.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_covar - calculates and diagonalizes the covariance matrix -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_covar\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_current.1 b/man/man1/g_current.1 index dda3b71a12..a69fc081ba 100644 --- a/man/man1/g_current.1 +++ b/man/man1/g_current.1 @@ -1,8 +1,8 @@ -.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_current - calculate current autocorrelation function of system -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_current\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_density.1 b/man/man1/g_density.1 index e86623db52..ec2ac27a22 100644 --- a/man/man1/g_density.1 +++ b/man/man1/g_density.1 @@ -1,8 +1,8 @@ -.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_density - calculates the density of the system -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_density\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_densmap.1 b/man/man1/g_densmap.1 index 96b59fe837..d2ba3ea184 100644 --- a/man/man1/g_densmap.1 +++ b/man/man1/g_densmap.1 @@ -1,8 +1,8 @@ -.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_densmap - calculates 2D planar or axial-radial density maps -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_densmap\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_densorder.1 b/man/man1/g_densorder.1 new file mode 100644 index 0000000000..af70bc445f --- /dev/null +++ b/man/man1/g_densorder.1 @@ -0,0 +1,123 @@ +.TH g_densorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" +.SH NAME +g_densorder - calculate surface fluctuations + +.B VERSION 4.5.4-dev-20110404-bc5695c +.SH SYNOPSIS +\f3g_densorder\fP +.BI "\-s" " topol.tpr " +.BI "\-f" " traj.xtc " +.BI "\-n" " index.ndx " +.BI "\-o" " Density4D.dat " +.BI "\-or" " hello.out " +.BI "\-og" " interface.xpm " +.BI "\-Spect" " intfspect.out " +.BI "\-[no]h" "" +.BI "\-[no]version" "" +.BI "\-nice" " int " +.BI "\-b" " time " +.BI "\-e" " time " +.BI "\-dt" " time " +.BI "\-[no]w" "" +.BI "\-[no]1d" "" +.BI "\-bw" " real " +.BI "\-bwn" " real " +.BI "\-order" " int " +.BI "\-axis" " string " +.BI "\-method" " enum " +.BI "\-d1" " real " +.BI "\-d2" " real " +.BI "\-tblock" " int " +.BI "\-nlevel" " int " +.SH 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 +.SH FILES +.BI "\-s" " topol.tpr" +.B Input + Run input file: tpr tpb tpa + +.BI "\-f" " traj.xtc" +.B Input + Trajectory: xtc trr trj gro g96 pdb cpt + +.BI "\-n" " index.ndx" +.B Input + Index file + +.BI "\-o" " Density4D.dat" +.B Output, Opt. + Generic data file + +.BI "\-or" " hello.out" +.B Output, Opt., Mult. + Generic output file + +.BI "\-og" " interface.xpm" +.B Output, Opt., Mult. + X PixMap compatible matrix file + +.BI "\-Spect" " intfspect.out" +.B Output, Opt., Mult. + Generic output file + +.SH OTHER OPTIONS +.BI "\-[no]h" "no " + Print help info and quit + +.BI "\-[no]version" "no " + Print version info and quit + +.BI "\-nice" " int" " 0" + Set the nicelevel + +.BI "\-b" " time" " 0 " + First frame (ps) to read from trajectory + +.BI "\-e" " time" " 0 " + Last frame (ps) to read from trajectory + +.BI "\-dt" " time" " 0 " + Only use frame when t MOD dt = first time (ps) + +.BI "\-[no]w" "no " + View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files + +.BI "\-[no]1d" "no " + Pseudo\-1d interface geometry + +.BI "\-bw" " real" " 0.2 " + Binwidth of density distribution tangential to interface + +.BI "\-bwn" " real" " 0.05 " + Binwidth of density distribution normal to interface + +.BI "\-order" " int" " 0" + Order of Gaussian filter, order 0 equates to NO filtering + +.BI "\-axis" " string" " Z" + Axis Direction \- X, Y or Z + +.BI "\-method" " enum" " bisect" + Interface location method: \fB bisect\fR or \fB functional\fR + +.BI "\-d1" " real" " 0 " + Bulk density phase 1 (at small z) + +.BI "\-d2" " real" " 1000 " + Bulk density phase 2 (at large z) + +.BI "\-tblock" " int" " 100" + Number of frames in one time\-block average + +.BI "\-nlevel" " int" " 100" + Number of Height levels in 2D \- XPixMaps + +.SH SEE ALSO +.BR gromacs(7) + +More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>. diff --git a/man/man1/g_dielectric.1 b/man/man1/g_dielectric.1 index a3f24fd193..b14a35c830 100644 --- a/man/man1/g_dielectric.1 +++ b/man/man1/g_dielectric.1 @@ -1,8 +1,8 @@ -.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dielectric - calculates frequency dependent dielectric constants -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dielectric\fP .BI "\-f" " dipcorr.xvg " @@ -125,16 +125,16 @@ g_dielectric - calculates frequency dependent dielectric constants Start value for fit parameter A .BI "\-tau1" " real" " 10 " - Start value for fit parameter [GRK]tau[grk]1 + Start value for fit parameter tau1 .BI "\-tau2" " real" " 1 " - Start value for fit parameter [GRK]tau[grk]2 + Start value for fit parameter tau2 .BI "\-eps0" " real" " 80 " - [GRK]epsilon[grk]0 of your liquid + epsilon0 of your liquid .BI "\-epsRF" " real" " 78.5 " - [GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity. + epsilon 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) diff --git a/man/man1/g_dih.1 b/man/man1/g_dih.1 index 76bd72b8c1..7ab738a44d 100644 --- a/man/man1/g_dih.1 +++ b/man/man1/g_dih.1 @@ -1,8 +1,8 @@ -.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dih - analyzes dihedral transitions -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dih\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_dipoles.1 b/man/man1/g_dipoles.1 index a3b6ae7927..3e0721ff6b 100644 --- a/man/man1/g_dipoles.1 +++ b/man/man1/g_dipoles.1 @@ -1,8 +1,8 @@ -.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dipoles - computes the total dipole plus fluctuations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dipoles\fP .BI "\-en" " ener.edr " @@ -99,7 +99,7 @@ g_dipoles - computes the total dipole plus fluctuations \&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 [GRK]epsilon[grk]RF of infinity (default), temperature of 300 K (default) and +\&using an epsilonRF 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 @@ -211,7 +211,7 @@ 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 [GRK]theta[grk]| between all pairs of molecules. May be slow + Calculate |cos theta| 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 molecules in one group, or between molecules in two different groups. This turns on the \fB \-gkr\fR flag. diff --git a/man/man1/g_disre.1 b/man/man1/g_disre.1 index 9aec1eb521..c384783af6 100644 --- a/man/man1/g_disre.1 +++ b/man/man1/g_disre.1 @@ -1,8 +1,8 @@ -.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_disre - analyzes distance restraints -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_disre\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_dist.1 b/man/man1/g_dist.1 index 95a34a456c..eb14147333 100644 --- a/man/man1/g_dist.1 +++ b/man/man1/g_dist.1 @@ -1,8 +1,8 @@ -.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dist - calculates the distances between the centers of mass of two groups -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dist\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_dyndom.1 b/man/man1/g_dyndom.1 index 577fde8064..e66b5b28be 100644 --- a/man/man1/g_dyndom.1 +++ b/man/man1/g_dyndom.1 @@ -1,8 +1,8 @@ -.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dyndom - interpolate and extrapolate structure rotations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dyndom\fP .BI "\-f" " dyndom.pdb " diff --git a/man/man1/g_enemat.1 b/man/man1/g_enemat.1 index 6f638ee221..02436048c3 100644 --- a/man/man1/g_enemat.1 +++ b/man/man1/g_enemat.1 @@ -1,8 +1,8 @@ -.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_enemat - extracts an energy matrix from an energy file -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_enemat\fP .BI "\-f" " ener.edr " diff --git a/man/man1/g_energy.1 b/man/man1/g_energy.1 index 617df4e23f..3d05b1b5a9 100644 --- a/man/man1/g_energy.1 +++ b/man/man1/g_energy.1 @@ -1,8 +1,8 @@ -.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_energy - writes energies to xvg files and displays averages -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_energy\fP .BI "\-f" " ener.edr " @@ -109,9 +109,9 @@ g_energy - writes energies to xvg files and displays averages \&With \fB \-fee\fR an estimate is calculated for the free\-energy \&difference with an ideal gas state: -\& [GRK]Delta[grk] A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT) +\& Delta A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT) -\& [GRK]Delta[grk] G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT) +\& Delta 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). @@ -120,9 +120,9 @@ g_energy - writes energies to xvg files and displays averages \&and using the potential energy. This also allows for an entropy \&estimate using: -\& [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,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- Delta A)/T -\& [GRK]Delta[grk] S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- [GRK]Delta[grk] G)/T +\& Delta S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- Delta G)/T \& diff --git a/man/man1/g_filter.1 b/man/man1/g_filter.1 index c662bef582..1945b9f06e 100644 --- a/man/man1/g_filter.1 +++ b/man/man1/g_filter.1 @@ -1,8 +1,8 @@ -.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_filter - frequency filters trajectories, useful for making smooth movies -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_filter\fP .BI "\-f" " traj.xtc " @@ -23,7 +23,7 @@ g_filter - frequency filters trajectories, useful for making smooth movies .BI "\-[no]fit" "" .SH DESCRIPTION \&\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 +\&The filter shape is cos(pi 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. diff --git a/man/man1/g_gyrate.1 b/man/man1/g_gyrate.1 index ef57f01582..bc101254c5 100644 --- a/man/man1/g_gyrate.1 +++ b/man/man1/g_gyrate.1 @@ -1,8 +1,8 @@ -.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_gyrate - calculates the radius of gyration -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_gyrate\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_h2order.1 b/man/man1/g_h2order.1 index 7295c29307..e3f2820a62 100644 --- a/man/man1/g_h2order.1 +++ b/man/man1/g_h2order.1 @@ -1,8 +1,8 @@ -.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_h2order - computes the orientation of water molecules -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_h2order\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_hbond.1 b/man/man1/g_hbond.1 index 9f1b3f5a93..9d2e3eb57f 100644 --- a/man/man1/g_hbond.1 +++ b/man/man1/g_hbond.1 @@ -1,8 +1,8 @@ -.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_hbond - computes and analyzes hydrogen bonds -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_hbond\fP .BI "\-f" " traj.xtc " @@ -249,7 +249,7 @@ g_hbond - computes and analyzes hydrogen bonds 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/[GRK]tau[grk]) + If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau) .BI "\-dump" " int" " 0" Dump the first N hydrogen bond ACFs in a single \fB .xvg\fR file for debugging diff --git a/man/man1/g_helix.1 b/man/man1/g_helix.1 index 4bacd85b44..0151fc0c50 100644 --- a/man/man1/g_helix.1 +++ b/man/man1/g_helix.1 @@ -1,8 +1,8 @@ -.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_helix - calculates basic properties of alpha helices -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_helix\fP .BI "\-s" " topol.tpr " @@ -29,24 +29,24 @@ g_helix - calculates basic properties of alpha helices .SH DESCRIPTION \&\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. +\&hydrogen bonds and phi/psi angles. \&That bit is fitted \&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 \fB radius.xvg\fR). This is merely the -\&RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms. +\&RMS deviation in two dimensions for all Calpha 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 \fB twist.xvg\fR). The average helical angle per -\&residue is calculated. For an [GRK]alpha[grk]\-helix it is 100 degrees, +\&residue is calculated. For an alpha\-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 \fB rise.xvg\fR). The helical rise per -\&residue is plotted as the difference in \fI z\fR\-coordinate between C[GRK]alpha[grk] +\&residue is plotted as the difference in \fI z\fR\-coordinate between Calpha \&atoms. For an ideal helix, this is 0.15 nm \&\fB 4.\fR Total helix length (file \fB len\-ahx.xvg\fR). The total length @@ -59,12 +59,12 @@ g_helix - calculates basic properties of alpha helices \&\fB 6.\fR Helix dipole, backbone only (file \fB dip\-ahx.xvg\fR). -\&\fB 7.\fR RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk] +\&\fB 7.\fR RMS deviation from ideal helix, calculated for the Calpha \&atoms only (file \fB rms\-ahx.xvg\fR). -\&\fB 8.\fR Average C[GRK]alpha[grk] \- C[GRK]alpha[grk] dihedral angle (file \fB phi\-ahx.xvg\fR). +\&\fB 8.\fR Average Calpha \- Calpha dihedral angle (file \fB phi\-ahx.xvg\fR). -\&\fB 9.\fR Average [GRK]phi[grk] and [GRK]psi[grk] angles (file \fB phipsi.xvg\fR). +\&\fB 9.\fR Average phi and psi angles (file \fB phipsi.xvg\fR). \&\fB 10.\fR Ellipticity at 222 nm according to Hirst and Brooks. \& diff --git a/man/man1/g_helixorient.1 b/man/man1/g_helixorient.1 index 6bcc4df1df..11d6320da8 100644 --- a/man/man1/g_helixorient.1 +++ b/man/man1/g_helixorient.1 @@ -1,8 +1,8 @@ -.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_helixorient - calculates local pitch/bending/rotation/orientation inside helices -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_helixorient\fP .BI "\-s" " topol.tpr " @@ -28,11 +28,11 @@ g_helixorient - calculates local pitch/bending/rotation/orientation inside helic .SH DESCRIPTION \&\fB g_helixorient\fR calculates the coordinates and direction of the average \&axis inside an alpha helix, and the direction/vectors of both the -\&C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis. +\&Calpha and (optionally) a sidechain atom relative to the axis. -\&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 +\&As input, you need to specify an index group with Calpha atoms +\&corresponding to an alpha\-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. @@ -40,12 +40,12 @@ g_helixorient - calculates local pitch/bending/rotation/orientation inside helic \&\fB Note\fR that this program does not do any fitting of structures. -\&We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix +\&We need four Calpha 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 \fI x\fR\-axis, the residues/C[GRK]alpha[grk] vector as \fI y\fR, and the +\&the helix axis as the local \fI x\fR\-axis, the residues/Calpha 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 diff --git a/man/man1/g_lie.1 b/man/man1/g_lie.1 index 18405a3ba3..7dddb0e682 100644 --- a/man/man1/g_lie.1 +++ b/man/man1/g_lie.1 @@ -1,8 +1,8 @@ -.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_lie - free energy estimate from linear combinations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_lie\fP .BI "\-f" " ener.edr " diff --git a/man/man1/g_mdmat.1 b/man/man1/g_mdmat.1 index 49be8f0cf5..c4b84e948b 100644 --- a/man/man1/g_mdmat.1 +++ b/man/man1/g_mdmat.1 @@ -1,8 +1,8 @@ -.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_mdmat - calculates residue contact maps -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_mdmat\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_membed.1 b/man/man1/g_membed.1 index 5cf08d2aa8..00702588ea 100644 --- a/man/man1/g_membed.1 +++ b/man/man1/g_membed.1 @@ -1,8 +1,8 @@ -.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_membed - embeds a protein into a lipid bilayer -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_membed\fP .BI "\-f" " into_mem.tpr " diff --git a/man/man1/g_mindist.1 b/man/man1/g_mindist.1 index 28827102f2..a07a6f030e 100644 --- a/man/man1/g_mindist.1 +++ b/man/man1/g_mindist.1 @@ -1,8 +1,8 @@ -.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_mindist - calculates the minimum distance between two groups -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_mindist\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_morph.1 b/man/man1/g_morph.1 index d98312babf..31c44c2449 100644 --- a/man/man1/g_morph.1 +++ b/man/man1/g_morph.1 @@ -1,8 +1,8 @@ -.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_morph - linear interpolation of conformations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_morph\fP .BI "\-f1" " conf1.gro " diff --git a/man/man1/g_msd.1 b/man/man1/g_msd.1 index d6ba62758c..95cdad029d 100644 --- a/man/man1/g_msd.1 +++ b/man/man1/g_msd.1 @@ -1,8 +1,8 @@ -.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_msd - calculates mean square displacements -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_msd\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_nmeig.1 b/man/man1/g_nmeig.1 index 5993d2d358..4bca624347 100644 --- a/man/man1/g_nmeig.1 +++ b/man/man1/g_nmeig.1 @@ -1,8 +1,8 @@ -.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_nmeig - diagonalizes the Hessian -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_nmeig\fP .BI "\-f" " hessian.mtx " diff --git a/man/man1/g_nmens.1 b/man/man1/g_nmens.1 index 746720ecf5..88f72fde13 100644 --- a/man/man1/g_nmens.1 +++ b/man/man1/g_nmens.1 @@ -1,8 +1,8 @@ -.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_nmens - generates an ensemble of structures from the normal modes -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_nmens\fP .BI "\-v" " eigenvec.trr " diff --git a/man/man1/g_nmtraj.1 b/man/man1/g_nmtraj.1 index 3363316cb0..b4fe86b2b6 100644 --- a/man/man1/g_nmtraj.1 +++ b/man/man1/g_nmtraj.1 @@ -1,8 +1,8 @@ -.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_nmtraj - generate a virtual trajectory from an eigenvector -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_nmtraj\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_order.1 b/man/man1/g_order.1 index 3e4267605a..e29acbdda0 100644 --- a/man/man1/g_order.1 +++ b/man/man1/g_order.1 @@ -1,8 +1,8 @@ -.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_order - computes the order parameter per atom for carbon tails -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_order\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_polystat.1 b/man/man1/g_polystat.1 index 8587c0891b..cebc497f18 100644 --- a/man/man1/g_polystat.1 +++ b/man/man1/g_polystat.1 @@ -1,8 +1,8 @@ -.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_polystat - calculates static properties of polymers -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_polystat\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_potential.1 b/man/man1/g_potential.1 index 6f928eeca4..aee31ae7e6 100644 --- a/man/man1/g_potential.1 +++ b/man/man1/g_potential.1 @@ -1,8 +1,8 @@ -.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_potential - calculates the electrostatic potential across the box -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_potential\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_principal.1 b/man/man1/g_principal.1 index 08ff893b48..5f353e1eb0 100644 --- a/man/man1/g_principal.1 +++ b/man/man1/g_principal.1 @@ -1,8 +1,8 @@ -.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_principal - calculates axes of inertia for a group of atoms -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_principal\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_protonate.1 b/man/man1/g_protonate.1 index 6ee442111a..c18fa870a8 100644 --- a/man/man1/g_protonate.1 +++ b/man/man1/g_protonate.1 @@ -1,8 +1,8 @@ -.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_protonate - protonates structures -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_protonate\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_rama.1 b/man/man1/g_rama.1 index a391744237..df19aafa0e 100644 --- a/man/man1/g_rama.1 +++ b/man/man1/g_rama.1 @@ -1,8 +1,8 @@ -.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rama - computes Ramachandran plots -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .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 -\&\fB g_rama\fR selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file +\&\fB g_rama\fR selects the phi/psi 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. diff --git a/man/man1/g_rdf.1 b/man/man1/g_rdf.1 index 2bc97b99e6..4f19f52a95 100644 --- a/man/man1/g_rdf.1 +++ b/man/man1/g_rdf.1 @@ -1,8 +1,8 @@ -.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rdf - calculates radial distribution functions -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rdf\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_rms.1 b/man/man1/g_rms.1 index 5cdb82af91..4ae7172710 100644 --- a/man/man1/g_rms.1 +++ b/man/man1/g_rms.1 @@ -1,8 +1,8 @@ -.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rms - calculates rmsd's with a reference structure and rmsd matrices -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rms\fP .BI "\-s" " topol.tpr " @@ -41,8 +41,8 @@ g_rms - calculates rmsd's with a reference structure and rmsd matrices .BI "\-ng" " int " .SH DESCRIPTION \&\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), +\&deviation (RMSD), the size\-independent rho similarity parameter +\&(\fB rho\fR) or the scaled rho (\fB rhosc\fR), \&see Maiorov & Crippen, Proteins \fB 22\fR, 273 (1995). \&This is selected by \fB \-what\fR. diff --git a/man/man1/g_rmsdist.1 b/man/man1/g_rmsdist.1 index 21fe01f490..a04194ac9c 100644 --- a/man/man1/g_rmsdist.1 +++ b/man/man1/g_rmsdist.1 @@ -1,8 +1,8 @@ -.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6 -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rmsdist\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_rmsf.1 b/man/man1/g_rmsf.1 index 88687c5695..943f195a96 100644 --- a/man/man1/g_rmsf.1 +++ b/man/man1/g_rmsf.1 @@ -1,8 +1,8 @@ -.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rmsf - calculates atomic fluctuations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rmsf\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_rotacf.1 b/man/man1/g_rotacf.1 index 84e6d6fb6b..0285ff01d7 100644 --- a/man/man1/g_rotacf.1 +++ b/man/man1/g_rotacf.1 @@ -1,8 +1,8 @@ -.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rotacf - calculates the rotational correlation function for molecules -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rotacf\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_rotmat.1 b/man/man1/g_rotmat.1 index b4b836fb99..36b32828ae 100644 --- a/man/man1/g_rotmat.1 +++ b/man/man1/g_rotmat.1 @@ -1,8 +1,8 @@ -.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_rotmat - plots the rotation matrix for fitting to a reference structure -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_rotmat\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_saltbr.1 b/man/man1/g_saltbr.1 index 197fdf528f..505774ffea 100644 --- a/man/man1/g_saltbr.1 +++ b/man/man1/g_saltbr.1 @@ -1,8 +1,8 @@ -.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_saltbr - computes salt bridges -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_saltbr\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_sas.1 b/man/man1/g_sas.1 index 657a7f61f0..3f5e400202 100644 --- a/man/man1/g_sas.1 +++ b/man/man1/g_sas.1 @@ -1,8 +1,8 @@ -.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sas - computes solvent accessible surface area -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sas\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_select.1 b/man/man1/g_select.1 index f94073003d..5be419804e 100644 --- a/man/man1/g_select.1 +++ b/man/man1/g_select.1 @@ -1,8 +1,8 @@ -.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_select - selects groups of atoms based on flexible textual selections -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_select\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_sgangle.1 b/man/man1/g_sgangle.1 index 251efc0603..d4f551e054 100644 --- a/man/man1/g_sgangle.1 +++ b/man/man1/g_sgangle.1 @@ -1,8 +1,8 @@ -.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sgangle - computes the angle and distance between two groups -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sgangle\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_sham.1 b/man/man1/g_sham.1 index 03b81292de..168cf7bcf6 100644 --- a/man/man1/g_sham.1 +++ b/man/man1/g_sham.1 @@ -1,8 +1,8 @@ -.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sham - read/write xmgr and xvgr data sets -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sham\fP .BI "\-f" " graph.xvg " diff --git a/man/man1/g_sigeps.1 b/man/man1/g_sigeps.1 index 868479e92e..7934223ea3 100644 --- a/man/man1/g_sigeps.1 +++ b/man/man1/g_sigeps.1 @@ -1,8 +1,8 @@ -.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sigeps\fP .BI "\-o" " potje.xvg " @@ -24,7 +24,7 @@ g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon .BI "\-sigfac" " real " .SH DESCRIPTION \&\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 +\&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. .SH FILES diff --git a/man/man1/g_sorient.1 b/man/man1/g_sorient.1 index 42b95d4123..8bd1cd82d9 100644 --- a/man/man1/g_sorient.1 +++ b/man/man1/g_sorient.1 @@ -1,8 +1,8 @@ -.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sorient - analyzes solvent orientation around solutes -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sorient\fP .BI "\-f" " traj.xtc " @@ -34,10 +34,10 @@ g_sorient - analyzes solvent orientation around solutes \&reference positions to the first atom of each solvent molecule: -\&[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent +\&theta1: the angle with the vector from the first atom of the solvent \&molecule to the midpoint between atoms 2 and 3. -\&[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the +\&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, \&the angle with the vector between atoms 2 and 3. @@ -49,18 +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([GRK]theta[grk]1) for rmin=r=rmax. +\&\fB \-o\fR: distribtion of cos(theta1) for rmin=r=rmax. -\&\fB \-no\fR: distribution of cos([GRK]theta[grk]2) for rmin=r=rmax. +\&\fB \-no\fR: distribution of cos(theta2) for rmin=r=rmax. -\&\fB \-ro\fR: cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of the +\&\fB \-ro\fR: cos(theta1) and 3cos2(theta2)\-1 as a function of the \&distance. \&\fB \-co\fR: the sum over all solvent molecules within distance r -\&of cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of r. +\&of cos(theta1) and 3cos2(theta2)\-1 as a function of r. \&\fB \-rc\fR: the distribution of the solvent molecules as a function of r diff --git a/man/man1/g_spatial.1 b/man/man1/g_spatial.1 index fae821ba17..46439a6b98 100644 --- a/man/man1/g_spatial.1 +++ b/man/man1/g_spatial.1 @@ -1,8 +1,8 @@ -.TH g_spatial 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_spatial 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_spatial - calculates the spatial distribution function -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_spatial\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/g_spol.1 b/man/man1/g_spol.1 index e5d24c82ad..4aca26b3fe 100644 --- a/man/man1/g_spol.1 +++ b/man/man1/g_spol.1 @@ -1,8 +1,8 @@ -.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_spol - analyzes solvent dipole orientation and polarization around solutes -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_spol\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_tcaf.1 b/man/man1/g_tcaf.1 index f9d48b1e9a..c208f14e2e 100644 --- a/man/man1/g_tcaf.1 +++ b/man/man1/g_tcaf.1 @@ -1,8 +1,8 @@ -.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_tcaf - calculates viscosities of liquids -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_tcaf\fP .BI "\-f" " traj.trr " @@ -34,7 +34,7 @@ g_tcaf - calculates viscosities of liquids .BI "\-endfit" " real " .SH DESCRIPTION \&\fB g_tcaf\fR computes tranverse current autocorrelations. -\&These are used to estimate the shear viscosity, [GRK]eta[grk]. +\&These are used to estimate the shear viscosity, eta. \&For details see: Palmer, Phys. Rev. E 49 (1994) pp 359\-366. @@ -47,10 +47,10 @@ g_tcaf - calculates viscosities of liquids \&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 [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 +\&v = \-t/(2 tau), W = sqrt(1 \- 4 tau eta/rho k2), which gives 16 values of tau +\&and eta. The fit weights decay with time as exp(\-t/wt), and the TCAF and \&fit are calculated up to time 5*wt. -\&The [GRK]eta[grk] values should be fitted to 1 \- a [GRK]eta[grk](k) k2, from which +\&The eta values should be fitted to 1 \- a eta(k) k2, from which \&one can estimate the shear viscosity at k=0. @@ -58,7 +58,7 @@ g_tcaf - calculates viscosities of liquids \&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 [GRK]eta[grk] estimates are also written to \fB \-ov\fR. +\&The cubic eta estimates are also written to \fB \-ov\fR. \&With option \fB \-mol\fR, the transverse current is determined of @@ -67,7 +67,7 @@ g_tcaf - calculates viscosities of liquids \&The k\-dependent viscosities in the \fB \-ov\fR file should be -\&fitted to [GRK]eta[grk](k) = [GRK]eta[grk]0 (1 \- a k2) to obtain the viscosity at +\&fitted to eta(k) = eta0 (1 \- a k2) to obtain the viscosity at \&infinite wavelength. diff --git a/man/man1/g_traj.1 b/man/man1/g_traj.1 index 1d8f8e82be..3b1d73b57e 100644 --- a/man/man1/g_traj.1 +++ b/man/man1/g_traj.1 @@ -1,8 +1,8 @@ -.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_traj\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_tune_pme.1 b/man/man1/g_tune_pme.1 index 59c4f7264a..fe62f5a69b 100644 --- a/man/man1/g_tune_pme.1 +++ b/man/man1/g_tune_pme.1 @@ -1,8 +1,8 @@ -.TH g_tune_pme 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_tune_pme 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_tune_pme - time mdrun as a function of PME nodes to optimize settings -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_tune_pme\fP .BI "\-p" " perf.out " diff --git a/man/man1/g_vanhove.1 b/man/man1/g_vanhove.1 index c88a6933c1..4008a1a787 100644 --- a/man/man1/g_vanhove.1 +++ b/man/man1/g_vanhove.1 @@ -1,8 +1,8 @@ -.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_vanhove - calculates Van Hove displacement functions -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_vanhove\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/g_velacc.1 b/man/man1/g_velacc.1 index a656d115f0..6a25e5280c 100644 --- a/man/man1/g_velacc.1 +++ b/man/man1/g_velacc.1 @@ -1,8 +1,8 @@ -.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_velacc - calculates velocity autocorrelation functions -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_velacc\fP .BI "\-f" " traj.trr " diff --git a/man/man1/g_wham.1 b/man/man1/g_wham.1 index 0adcaa5502..ffb9ae4491 100644 --- a/man/man1/g_wham.1 +++ b/man/man1/g_wham.1 @@ -1,8 +1,8 @@ -.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_wham - weighted histogram analysis after umbrella sampling -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_wham\fP .BI "\-ix" " pullx\-files.dat " @@ -150,13 +150,13 @@ g_wham - weighted histogram analysis after umbrella sampling \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- \&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 +\&time (IACT) tau for each umbrella window and weights the respective +\&window with 1/[1+2*tau/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, +\&reaction coordinate with a Gaussian (sigma 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 @@ -329,7 +329,7 @@ Bootstrapping output: Calculate integrated autocorrelation times and use in wham .BI "\-acsig" " real" " 0 " - Smooth autocorrelation times along reaction coordinate with Gaussian of this [GRK]sigma[grk] + Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma .BI "\-ac\-trestart" " real" " 1 " When computing autocorrelation functions, restart computing every .. (ps) diff --git a/man/man1/g_wheel.1 b/man/man1/g_wheel.1 index 5207ea39a3..4f9a6ec952 100644 --- a/man/man1/g_wheel.1 +++ b/man/man1/g_wheel.1 @@ -1,8 +1,8 @@ -.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_wheel - plots helical wheels -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_wheel\fP .BI "\-f" " nnnice.dat " diff --git a/man/man1/g_x2top.1 b/man/man1/g_x2top.1 index 5bb14a22e1..b99fc16d82 100644 --- a/man/man1/g_x2top.1 +++ b/man/man1/g_x2top.1 @@ -1,8 +1,8 @@ -.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_x2top - generates a primitive topology from coordinates -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_x2top\fP .BI "\-f" " conf.gro " diff --git a/man/man1/g_xrama.1 b/man/man1/g_xrama.1 index e0360b3949..6f741e9691 100644 --- a/man/man1/g_xrama.1 +++ b/man/man1/g_xrama.1 @@ -1,8 +1,8 @@ -.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_xrama - shows animated Ramachandran plots -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_xrama\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/genbox.1 b/man/man1/genbox.1 index 2ec3d33b73..c573dbf155 100644 --- a/man/man1/genbox.1 +++ b/man/man1/genbox.1 @@ -1,8 +1,8 @@ -.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME genbox - solvates a system -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3genbox\fP .BI "\-cp" " protein.gro " diff --git a/man/man1/genconf.1 b/man/man1/genconf.1 index 85a8d6d780..280008f3c9 100644 --- a/man/man1/genconf.1 +++ b/man/man1/genconf.1 @@ -1,8 +1,8 @@ -.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME genconf - multiplies a conformation in 'random' orientations -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3genconf\fP .BI "\-f" " conf.gro " diff --git a/man/man1/genion.1 b/man/man1/genion.1 index 6cb4dcf8e9..748b7d13ad 100644 --- a/man/man1/genion.1 +++ b/man/man1/genion.1 @@ -1,8 +1,8 @@ -.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME genion - generates mono atomic ions on energetically favorable positions -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3genion\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/genrestr.1 b/man/man1/genrestr.1 index 37992dce4e..fde0d40d50 100644 --- a/man/man1/genrestr.1 +++ b/man/man1/genrestr.1 @@ -1,8 +1,8 @@ -.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME genrestr - generates position restraints or distance restraints for index groups -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3genrestr\fP .BI "\-f" " conf.gro " @@ -42,7 +42,7 @@ genrestr - generates position restraints or distance restraints for index groups \&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[GRK]alpha[grk] atoms in a protein, one can +\&one typically would apply to Calpha 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 diff --git a/man/man1/gmxcheck.1 b/man/man1/gmxcheck.1 index 4eb4b6fb4c..08bc3a07d4 100644 --- a/man/man1/gmxcheck.1 +++ b/man/man1/gmxcheck.1 @@ -1,8 +1,8 @@ -.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME gmxcheck - checks and compares files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3gmxcheck\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/gmxdump.1 b/man/man1/gmxdump.1 index 2be6f6cd58..70daa77b18 100644 --- a/man/man1/gmxdump.1 +++ b/man/man1/gmxdump.1 @@ -1,8 +1,8 @@ -.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME gmxdump - makes binary files human readable -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3gmxdump\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/grompp.1 b/man/man1/grompp.1 index f6221e3e2b..ff1b1214d5 100644 --- a/man/man1/grompp.1 +++ b/man/man1/grompp.1 @@ -1,8 +1,8 @@ -.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME grompp - makes a run input file -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3grompp\fP .BI "\-f" " grompp.mdp " diff --git a/man/man1/make_edi.1 b/man/man1/make_edi.1 index e81709f178..28c40cf727 100644 --- a/man/man1/make_edi.1 +++ b/man/man1/make_edi.1 @@ -1,8 +1,8 @@ -.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME make_edi - generate input files for essential dynamics sampling -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3make_edi\fP .BI "\-f" " eigenvec.trr " @@ -154,7 +154,7 @@ You will be prompted for one or more index groups that correspond to the eigenve \&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 [GRK]tau[grk] means slow adaption (i.e. growth). +\&Tau is the time constant of adaptive flooding, high tau 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 \fB \-tau\fR to zero. \& @@ -162,9 +162,9 @@ You will be prompted for one or more index groups that correspond to the eigenve \&\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. -\&[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. +\&alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would +\&increase, this is mimicked by alpha 1. +\&For restraining, alpha 1 can give you smaller width in the restraining potential. \& diff --git a/man/man1/make_ndx.1 b/man/man1/make_ndx.1 index 36b0f1cd3b..fca42008bb 100644 --- a/man/man1/make_ndx.1 +++ b/man/man1/make_ndx.1 @@ -1,8 +1,8 @@ -.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME make_ndx - makes index files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3make_ndx\fP .BI "\-f" " conf.gro " diff --git a/man/man1/mdrun.1 b/man/man1/mdrun.1 index d476ec9c2c..8aaf75dd63 100644 --- a/man/man1/mdrun.1 +++ b/man/man1/mdrun.1 @@ -1,8 +1,8 @@ -.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME mdrun - performs a simulation, do a normal mode analysis or an energy minimization -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3mdrun\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/mk_angndx.1 b/man/man1/mk_angndx.1 index 2db4099443..e9bce82bef 100644 --- a/man/man1/mk_angndx.1 +++ b/man/man1/mk_angndx.1 @@ -1,8 +1,8 @@ -.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME mk_angndx - generates index files for g_angle -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3mk_angndx\fP .BI "\-s" " topol.tpr " diff --git a/man/man1/ngmx.1 b/man/man1/ngmx.1 index 118d45726a..0a4affc768 100644 --- a/man/man1/ngmx.1 +++ b/man/man1/ngmx.1 @@ -1,8 +1,8 @@ -.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME ngmx - displays a trajectory -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3ngmx\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/pdb2gmx.1 b/man/man1/pdb2gmx.1 index ae103de3af..dfa5d22e16 100644 --- a/man/man1/pdb2gmx.1 +++ b/man/man1/pdb2gmx.1 @@ -1,8 +1,8 @@ -.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME pdb2gmx - converts pdb files to topology and coordinate files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3pdb2gmx\fP .BI "\-f" " eiwit.pdb " diff --git a/man/man1/tpbconv.1 b/man/man1/tpbconv.1 index 15dcd4dd54..4515836ebe 100644 --- a/man/man1/tpbconv.1 +++ b/man/man1/tpbconv.1 @@ -1,8 +1,8 @@ -.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME tpbconv - makes a run input file for restarting a crashed run -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3tpbconv\fP .BI "\-s" " topol.tpr " @@ -42,7 +42,7 @@ tpbconv - makes a run input file for restarting a crashed run \&\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 \fB .tpx\fR file, or when you want to make e.g. a pure C[GRK]alpha[grk] \fB .tpx\fR file. +\&your \fB .tpx\fR file, or when you want to make e.g. a pure Calpha \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. diff --git a/man/man1/trjcat.1 b/man/man1/trjcat.1 index 55cb9694b5..105282d285 100644 --- a/man/man1/trjcat.1 +++ b/man/man1/trjcat.1 @@ -1,8 +1,8 @@ -.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME trjcat - concatenates trajectory files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3trjcat\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/trjconv.1 b/man/man1/trjconv.1 index 37d9729f0a..637edc2170 100644 --- a/man/man1/trjconv.1 +++ b/man/man1/trjconv.1 @@ -1,8 +1,8 @@ -.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME trjconv - converts and manipulates trajectory files -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3trjconv\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/trjorder.1 b/man/man1/trjorder.1 index d8c75c00e6..40a18cdd67 100644 --- a/man/man1/trjorder.1 +++ b/man/man1/trjorder.1 @@ -1,8 +1,8 @@ -.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME trjorder - orders molecules according to their distance to a group -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3trjorder\fP .BI "\-f" " traj.xtc " diff --git a/man/man1/xpm2ps.1 b/man/man1/xpm2ps.1 index 277efb3c2b..216d97fd82 100644 --- a/man/man1/xpm2ps.1 +++ b/man/man1/xpm2ps.1 @@ -1,8 +1,8 @@ -.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec" +.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME xpm2ps - converts XPM matrices to encapsulated postscript (or XPM) -.B VERSION 4.5.4-dev-20110404-3c0e5ec +.B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3xpm2ps\fP .BI "\-f" " root.xpm " -- 2.11.4.GIT