From 8c87e60d8b91764b730452e16365e3c2862f67a3 Mon Sep 17 00:00:00 2001 From: Roland Schulz Date: Fri, 6 Jul 2012 23:25:08 -0400 Subject: [PATCH] Autogenerate gromacs.7 from programs.txt Change-Id: I958906dc9967155bccd3f43e5a6882632a829951 --- cmake/BuildManPages.cmake | 35 +++++ man/man7/gromacs.7 | 375 --------------------------------------------- man/man7/gromacs.7.cmakein | 194 +++++++++++++++++++++++ 3 files changed, 229 insertions(+), 375 deletions(-) delete mode 100644 man/man7/gromacs.7 create mode 100644 man/man7/gromacs.7.cmakein diff --git a/cmake/BuildManPages.cmake b/cmake/BuildManPages.cmake index 6ee1b12ac8..7e308b5e12 100644 --- a/cmake/BuildManPages.cmake +++ b/cmake/BuildManPages.cmake @@ -1,7 +1,42 @@ +MACRO(TODAY RESULT) + IF(UNIX) + EXECUTE_PROCESS(COMMAND "date" "+%F" OUTPUT_VARIABLE ${RESULT} OUTPUT_STRIP_TRAILING_WHITESPACE) + ELSE() + set(${RESULT} "????-??-??") + ENDIF() +ENDMACRO(TODAY) + if(GMX_BUILD_MANPAGES) set(MAN1_PATH ${CMAKE_BINARY_DIR}/man/man1) file(MAKE_DIRECTORY ${MAN1_PATH}) + + #create gromacs.7 + FILE(READ "${CMAKE_SOURCE_DIR}/admin/programs.txt" contents) + + # Convert file contents into a CMake list. First escape ; + STRING(REGEX REPLACE ";" "\\\\;" contents "${contents}") + STRING(REGEX REPLACE "\n" ";" contents "${contents}") + + set(PROGMANPAGES "") + foreach(line ${contents}) + if (${line} MATCHES "^HEAD\\|") + string(REGEX REPLACE "^HEAD\\|" "" DESC ${line}) + set(PROGMANPAGES "${PROGMANPAGES}.Sh \"${DESC}\"\n.IX Subsection \"${DESC}\"\n.Vb\n.ta 16n\n") + elseif(${line} MATCHES "^END$") + set(PROGMANPAGES "${PROGMANPAGES}.Ve\n") + elseif(${line} MATCHES "\\|") + string(REGEX REPLACE "\\|" "\t" line ${line}) + set(PROGMANPAGES "${PROGMANPAGES}\\& ${line}\n") + else() + message(WARNING "Incorrectly formated line \"${line}\" in programs.txt") + endif() + endforeach() + TODAY(TODAYS_DATE) + configure_file(${CMAKE_SOURCE_DIR}/man/man7/gromacs.7.cmakein ${CMAKE_BINARY_DIR}/man/man7/gromacs.7) + install(FILES ${CMAKE_BINARY_DIR}/man/man7/gromacs.7 DESTINATION + ${MAN_INSTALL_DIR}/man7) endif() + function (gmx_add_man_page EXENAME) if(GMX_BUILD_MANPAGES) file(STRINGS ${CMAKE_SOURCE_DIR}/admin/programs.txt DESC diff --git a/man/man7/gromacs.7 b/man/man7/gromacs.7 deleted file mode 100644 index 7c9ee75eee..0000000000 --- a/man/man7/gromacs.7 +++ /dev/null @@ -1,375 +0,0 @@ -.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.14 -.\" (and then reused elsewhere, since this isn't a perl package) -.\" -.\" Standard preamble: -.\" ======================================================================== -.de Sh \" Subsection heading -.br -.if t .Sp -.ne 5 -.PP -\fB\\$1\fR -.PP -.. -.de Sp \" Vertical space (when we can't use .PP) -.if t .sp .5v -.if n .sp -.. -.de Vb \" Begin verbatim text -.ft CW -.nf -.ne \\$1 -.. -.de Ve \" End verbatim text -.ft R -.fi -.. -.\" Set up some character translations and predefined strings. \*(-- will -.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left -.\" double quote, and \*(R" will give a right double quote. | will give a -.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to -.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C' -.\" expand to `' in nroff, nothing in troff, for use with C<>. -.tr \(*W-|\(bv\*(Tr -.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' -.ie n \{\ -. ds -- \(*W- -. ds PI pi -. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch -. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch -. ds L" "" -. ds R" "" -. ds C` "" -. ds C' "" -'br\} -.el\{\ -. ds -- \|\(em\| -. ds PI \(*p -. ds L" `` -. ds R" '' -'br\} -.\" -.\" If the F register is turned on, we'll generate index entries on stderr for -.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index -.\" entries marked with X<> in POD. Of course, you'll have to process the -.\" output yourself in some meaningful fashion. -.if \nF \{\ -. de IX -. tm Index:\\$1\t\\n%\t"\\$2" -.. -. nr % 0 -. rr F -.\} -.\" -.\" For nroff, turn off justification. Always turn off hyphenation; it makes -.\" way too many mistakes in technical documents. -.hy 0 -.if n .na -.\" -.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). -.\" Fear. Run. Save yourself. No user-serviceable parts. -. \" fudge factors for nroff and troff -.if n \{\ -. ds #H 0 -. ds #V .8m -. ds #F .3m -. ds #[ \f1 -. ds #] \fP -.\} -.if t \{\ -. ds #H ((1u-(\\\\n(.fu%2u))*.13m) -. ds #V .6m -. ds #F 0 -. ds #[ \& -. ds #] \& -.\} -. \" simple accents for nroff and troff -.if n \{\ -. ds ' \& -. ds ` \& -. ds ^ \& -. ds , \& -. ds ~ ~ -. ds / -.\} -.if t \{\ -. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" -. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' -. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' -. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' -. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' -. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' -.\} -. \" troff and (daisy-wheel) nroff accents -.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' -.ds 8 \h'\*(#H'\(*b\h'-\*(#H' -.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] -.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' -.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' -.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] -.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] -.ds ae a\h'-(\w'a'u*4/10)'e -.ds Ae A\h'-(\w'A'u*4/10)'E -. \" corrections for vroff -.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' -.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' -. \" for low resolution devices (crt and lpr) -.if \n(.H>23 .if \n(.V>19 \ -\{\ -. ds : e -. ds 8 ss -. ds o a -. ds d- d\h'-1'\(ga -. ds D- D\h'-1'\(hy -. ds th \o'bp' -. ds Th \o'LP' -. ds ae ae -. ds Ae AE -.\} -.rm #[ #] #H #V #F C -.\" ======================================================================== -.\" -.IX Title "GROMACS 7" -.TH GROMACS 7 "2008-10-12" "gromacs" "GROMACS suite, Version 4.0" -.SH "NAME" -gromacs \- molecular dynamics simulation suite -.SH "DESCRIPTION" -.B GROMACS -(the Groningen Machine for Chemical Simulations) is a full-featured -suite of programs to perform molecular dynamics simulations - in other -words, to simulate the behavior of systems with hundreds to millions -of particles, using Newtonian equations of motion. It is primarily -used for research on proteins, lipids, and polymers, but can be applied -to a wide variety of chemical and biological research questions. -.SH "SYNOPSIS" -.IX Header "SYNOPSIS" -.PP -The following commands make up the GROMACS suite. Please refer to their -individual man pages for further details. -.Sh "Generating topologies and coordinates" -.IX Subsection "Generating topologies and coordinates" -.Vb 7 -\& pdb2gmx converts pdb files to topology and coordinate files -\& g_x2top generates a primitive topology from coordinates -\& editconf edits the box and writes subgroups -\& genbox solvates a system -\& genion generates mono atomic ions on energetically favorable positions -\& genconf multiplies a conformation in 'random' orientations -\& g_protonate protonates structures -.Ve -.Sh "Running a simulation" -.IX Subsection "Running a simulation" -.Vb 4 -\& grompp makes a run input file -\& tpbconv makes a run input file for restarting a crashed run -\& mdrun performs a simulation, do a normal mode analysis or an energy minimization -\& mdrun_mpi performs a sim across multiple CPUs or systems -.Ve -.Sh "Viewing trajectories" -.IX Subsection "Viewing trajectories" -.Vb 3 -\& ngmx displays a trajectory -\& g_highway X Window System gadget for highway simulations -\& g_nmtraj generate a virtual trajectory from an eigenvector -.Ve -.Sh "Processing energies" -.IX Subsection "Processing energies" -.Vb 3 -\& g_energy writes energies to xvg files and displays averages -\& g_enemat extracts an energy matrix from an energy file -\& mdrun with \-rerun (re)calculates energies for trajectory frames -.Ve -.Sh "Converting files" -.IX Subsection "Converting files" -.Vb 6 -\& editconf converts and manipulates structure files -\& trjconv converts and manipulates trajectory files -\& trjcat concatenates trajectory files -\& eneconv converts energy files -\& xpm2ps converts XPM matrices to encapsulated postscript (or XPM) -\& g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon -.Ve -.Sh "Tools" -.IX Subsection "Tools" -.Vb 18 -\& make_ndx makes index files -\& mk_angndx generates index files for g_angle -\& gmxcheck checks and compares files -\& gmxdump makes binary files human readable -\& g_traj plots x, v and f of selected atoms/groups (and more) from a trajectory -\& g_analyze analyzes data sets -\& trjorder orders molecules according to their distance to a group -\& g_filter frequency filters trajectories, useful for making smooth movies -\& g_lie free energy estimate from linear combinations -\& g_dyndom interpolate and extrapolate structure rotations -\& g_morph linear interpolation of conformations -\& g_wham weighted histogram analysis after umbrella sampling -\& xpm2ps convert XPM (XPixelMap) file to postscript -\& g_sham read/write xmgr and xvgr data sets -\& g_spatial calculates the spatial distribution function (more control than g_sdf) -\& g_sdf calculates the spatial distribution function (faster than g_spatial) -\& g_select selects groups of atoms based on flexible textual selections -\& g_tune_pme time mdrun as a function of PME nodes to optimize settings -.Ve -.Sh "Distances between structures" -.IX Subsection "Distances between structures" -.Vb 4 -\& g_rms calculates rmsd's with a reference structure and rmsd matrices -\& g_confrms fits two structures and calculates the rmsd -\& g_cluster clusters structures -\& g_rmsf calculates atomic fluctuations -.Ve -.Sh "Distances in structures over time" -.IX Subsection "Distances in structures over time" -.Vb 6 -\& g_mindist calculates the minimum distance between two groups -\& g_dist calculates the distances between the centers of mass of two groups -\& g_bond calculates distances between atoms -\& g_mdmat calculates residue contact maps -\& g_polystat calculates static properties of polymers -\& g_rmsdist calculates atom pair distances averaged with power \-2, \-3 or \-6 -.Ve -.Sh "Mass distribution properties over time" -.IX Subsection "Mass distribution properties over time" -.Vb 8 -\& g_traj plots x, v, f, box, temperature and rotational energy -\& g_gyrate calculates the radius of gyration -\& g_msd calculates mean square displacements -\& g_polystat calculates static properties of polymers -\& g_rotacf calculates the rotational correlation function for molecules -\& g_rdf calculates radial distribution functions -\& g_rotmat plots the rotation matrix for fitting to a reference structure -\& g_vanhove calculates Van Hove displacement functions -.Ve -.Sh "Analyzing bonded interactions" -.IX Subsection "Analyzing bonded interactions" -.Vb 4 -\& g_bond calculates bond length distributions -\& mk_angndx generates index files for g_angle -\& g_angle calculates distributions and correlations for angles and dihedrals -\& g_dih analyzes dihedral transitions -.Ve -.Sh "Structural properties" -.IX Subsection "Structural properties" -.Vb 14 -\& g_hbond computes and analyzes hydrogen bonds -\& g_saltbr computes salt bridges -\& g_sas computes solvent accessible surface area -\& g_order computes the order parameter per atom for carbon tails -\& g_principal calculates axes of inertia for a group of atoms -\& g_rdf calculates radial distribution functions -\& g_sdf calculates solvent distribution functions -\& g_sgangle computes the angle and distance between two groups -\& g_sorient analyzes solvent orientation around solutes -\& g_spol analyzes solvent dipole orientation and polarization around solutes -\& g_bundle analyzes bundles of axes, e.g. helices -\& g_disre analyzes distance restraints -\& g_clustsize calculate size distributions of atomic clusters -\& g_anadock cluster structures from Autodock runs -.Ve -.Sh "Kinetic properties" -.IX Subsection "Kinetic properties" -.Vb 8 -\& g_traj plots x, v, f, box, temperature and rotational energy -\& g_velacc calculates velocity autocorrelation functions -\& g_tcaf calculates viscosities of liquids -\& g_kinetics calculate kinetic rate constants (experimental) -\& g_bar calculates free energy difference estimates through Bennett's acceptance ratio -\& g_current calculate current autocorrelation function of system -\& g_vanhove compute Van Hove correlation function -\& g_principal calculate principal axes of inertion for a group of atoms -.Ve -.Sh "Electrostatic properties" -.IX Subsection "Electrostatic properties" -.Vb 6 -\& genion generates mono atomic ions on energetically favorable positions -\& g_potential calculates the electrostatic potential across the box -\& g_dipoles computes the total dipole plus fluctuations -\& g_dielectric calculates frequency dependent dielectric constants -\& g_current calculate current autocorrelation function of system -\& g_spol analyze dipoles around a solute -.Ve -.Sh "Protein specific analysis" -.IX Subsection "Protein specific analysis" -.Vb 7 -\& do_dssp assigns secondary structure and calculates solvent accessible surface area -\& g_chi calculates everything you want to know about chi and other dihedrals -\& g_helix calculates everything you want to know about helices -\& g_helixorient calculate coordinates/directions of alpha-helix components -\& g_rama computes Ramachandran plots -\& g_xrama shows animated Ramachandran plots -\& wheel plots helical wheels -.Ve -.Sh "Interfaces" -.IX Subsection "Interfaces" -.Vb 6 -\& g_potential calculates the electrostatic potential across the box -\& g_density calculates the density of the system -\& 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 -\& g_membed embeds a protein into a lipid bilayer -.Ve -.Sh "Covariance analysis" -.IX Subsection "Covariance analysis" -.Vb 3 -\& g_covar calculates and diagonalizes the covariance matrix -\& g_anaeig analyzes the eigenvectors -\& make_edi generate essential-dynamics input file from g_covar output -.Ve -.Sh "Normal modes" -.IX Subsection "Normal modes" -.Vb 7 -\& grompp makes a run input file -\& mdrun finds a potential energy minimum -\& mdrun calculates the Hessian -\& g_nmeig diagonalizes the Hessian -\& make_edi generates essential-dynamics input file from g_nmeig analysis -\& g_anaeig analyzes the normal modes -\& g_nmens generates an ensemble of structures from the normal modes -.Ve -.PP -.SH "ADDITIONAL DOCUMENTATION" -.IX Header "ADDITIONAL DOCUMENTATION" -Consult the manual at <\fIhttp://www.gromacs.org/content/view/27/42/\fR> for an -introduction to molecular dynamics in general and GROMACS in particular, -as well as an overview of the individual programs. -.PP -The shorter HTML reference and GROMACS FAQ are available in \fB/usr/share/doc/gromacs/html/\fR . -.PP -Tutorial files and other miscellaneous references are stored in \fB/usr/share/gromacs/\fR . -.SH "REFERENCES" -.IX Header "REFERENCES" -The development of GROMACS is mainly funded by academic research grants. -To help us fund development, the authors humbly ask that you cite the GROMACS papers: -.PP -H.J.C. Berendsen, D. van der Spoel and R. van Drunen. \fBGROMACS: A message-passing -parallel molecular dynamics implementation\fR. Comp. Phys. Comm. \fI91\fR, 43-56 (1995) -.PP -Erik Lindahl, Berk Hess and David van der Spoel. \fBGROMACS 3.0: A package for -molecular simulation and trajectory analysis\fR. J. Mol. Mod. \fI7\fR, 306-317 (2001) -.PP -B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. \fBGROMACS 4: Algorithms for -Highly Efficient, Load-Balanced, and Scalable Molecular Simulation\fR. J. Chem. Theory -Comput. \fI4\fR, 3, 435-447 (2008), <\fIhttp://dx.doi.org/10.1021/ct700301q\fR> -.SH "AUTHORS" -.IX Header "AUTHORS" -Current developers: -.PP -David van der Spoel -.br -Berk Hess -.br -Erik Lindahl -.PP -A full list of present and former contributors -is available at -.PP -This manual page is largely based on the GROMACS online reference, and was -prepared in this format by Nicholas Breen . -.SH "BUGS" -.IX Header "BUGS" -GROMACS has no major known bugs, but be warned that it stresses your CPU more -than most software. Systems with slightly flaky hardware may prove unreliable -while running heavy-duty simulations. If at all possible, please try to -reproduce bugs on another machine before reporting them. diff --git a/man/man7/gromacs.7.cmakein b/man/man7/gromacs.7.cmakein new file mode 100644 index 0000000000..aa17f1f4f9 --- /dev/null +++ b/man/man7/gromacs.7.cmakein @@ -0,0 +1,194 @@ +.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.14 +.\" (and then reused elsewhere, since this isn't a perl package) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sh \" Subsection heading +.br +.if t .Sp +.ne 5 +.PP +\fB\\$1\fR +.PP +.. +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. | will give a +.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to +.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C' +.\" expand to `' in nroff, nothing in troff, for use with C<>. +.tr \(*W-|\(bv\*(Tr +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.if \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.\" +.\" For nroff, turn off justification. Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.hy 0 +.if n .na +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.rm #[ #] #H #V #F C +.\" ======================================================================== +.\" +.IX Title "GROMACS 7" +.TH GROMACS 7 "${TODAYS_DATE}" "gromacs" "GROMACS suite, Version ${PROJECT_VERSION}" +.SH "NAME" +gromacs \- molecular dynamics simulation suite +.SH "DESCRIPTION" +.B GROMACS +(the Groningen Machine for Chemical Simulations) is a full-featured +suite of programs to perform molecular dynamics simulations - in other +words, to simulate the behavior of systems with hundreds to millions +of particles, using Newtonian equations of motion. It is primarily +used for research on proteins, lipids, and polymers, but can be applied +to a wide variety of chemical and biological research questions. +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +.PP +The following commands make up the GROMACS suite. Please refer to their +individual man pages for further details. +${PROGMANPAGES} +.PP +.SH "ADDITIONAL DOCUMENTATION" +.IX Header "ADDITIONAL DOCUMENTATION" +Consult the manual at <\fIhttp://www.gromacs.org/content/view/27/42/\fR> for an +introduction to molecular dynamics in general and GROMACS in particular, +as well as an overview of the individual programs. +.PP +The shorter HTML reference and GROMACS FAQ are available in \fB/usr/share/doc/gromacs/html/\fR . +.PP +Tutorial files and other miscellaneous references are stored in \fB/usr/share/gromacs/\fR . +.SH "REFERENCES" +.IX Header "REFERENCES" +The development of GROMACS is mainly funded by academic research grants. +To help us fund development, the authors humbly ask that you cite the GROMACS papers: +.PP +H.J.C. Berendsen, D. van der Spoel and R. van Drunen. \fBGROMACS: A message-passing +parallel molecular dynamics implementation\fR. Comp. Phys. Comm. \fI91\fR, 43-56 (1995) +.PP +Erik Lindahl, Berk Hess and David van der Spoel. \fBGROMACS 3.0: A package for +molecular simulation and trajectory analysis\fR. J. Mol. Mod. \fI7\fR, 306-317 (2001) +.PP +B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. \fBGROMACS 4: Algorithms for +Highly Efficient, Load-Balanced, and Scalable Molecular Simulation\fR. J. Chem. Theory +Comput. \fI4\fR, 3, 435-447 (2008), <\fIhttp://dx.doi.org/10.1021/ct700301q\fR> +.SH "AUTHORS" +.IX Header "AUTHORS" +Current developers: +.PP +David van der Spoel +.br +Berk Hess +.br +Erik Lindahl +.PP +A full list of present and former contributors +is available at +.PP +This manual page is largely based on the GROMACS online reference, and was +prepared in this format by Nicholas Breen . +.SH "BUGS" +.IX Header "BUGS" +GROMACS has no major known bugs, but be warned that it stresses your CPU more +than most software. Systems with slightly flaky hardware may prove unreliable +while running heavy-duty simulations. If at all possible, please try to +reproduce bugs on another machine before reporting them. -- 2.11.4.GIT