+++ /dev/null
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-\{\
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-.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 <spoel@gromacs.org>
-.br
-Berk Hess <hess@gromacs.org>
-.br
-Erik Lindahl <lindahl@gromacs.org>
-.PP
-A full list of present and former contributors
-is available at <http://www.gromacs.org>
-.PP
-This manual page is largely based on the GROMACS online reference, and was
-prepared in this format by Nicholas Breen <nbreen@ofb.net>.
-.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.
--- /dev/null
+.\" 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
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+\fB\\$1\fR
+.PP
+..
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+..
+.de Ve \" End verbatim text
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+..
+.\" Set up some character translations and predefined strings. \*(-- will
+.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
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+.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to
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+'br\}
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+. ds -- \|\(em\|
+. ds PI \(*p
+. ds L" ``
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+'br\}
+.\"
+.\" If the F register is turned on, we'll generate index entries on stderr for
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+.\" 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
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+. \" troff and (daisy-wheel) nroff accents
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+.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 <spoel@gromacs.org>
+.br
+Berk Hess <hess@gromacs.org>
+.br
+Erik Lindahl <lindahl@gromacs.org>
+.PP
+A full list of present and former contributors
+is available at <http://www.gromacs.org>
+.PP
+This manual page is largely based on the GROMACS online reference, and was
+prepared in this format by Nicholas Breen <nbreen@ofb.net>.
+.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.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff