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+.\" ========================================================================
+.\"
+.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
+\& 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
+\& 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
+\& mdrun_mpi performs a sim across multiple CPUs or systems (in separate package)
+.Ve
+.Sh "Viewing trajectories"
+.IX Subsection "Viewing trajectories"
+.Vb 3
+\& ngmx displays a trajectory
+\& trjconv converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
+\& 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 5
+\& 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)
+\& 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
+\& genrestr generate topology include file with position restraints
+\& 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_densmap compute 2D number-density maps and generate plots
+\& 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)
+.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 5
+\& 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_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 5
+\& 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_rotacf calculates the rotational correlation function for molecules
+\& g_rdf calculates radial distribution 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 11
+\& 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_sgangle computes the angle and distance between two groups
+\& g_sorient analyzes solvent orientation around solutes
+\& g_bundle analyzes bundles of axes, e.g. helices
+\& g_disre analyzes distance restraints
+\& g_clustsize calculate size distributions of atomic clusters
+\& anadock cluster structures from Autodock runs
+\& g_polystat plot average static properties of polymers
+.Ve
+.Sh "Kinetic properties"
+.IX Subsection "Kinetic properties"
+.Vb 7
+\& 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_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 5
+\& 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_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
+\& xrama shows animated Ramachandran plots
+\& wheel plots helical wheels
+.Ve
+.Sh "Interfaces"
+.IX Subsection "Interfaces"
+.Vb 5
+\& 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
+.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.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff