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GMX(1)				    GROMACS				GMX(1)

NAME
       gmx - molecular dynamics	simulation suite

SYNOPSIS
	  gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice _int_]
	      [-[no]backup]

DESCRIPTION
       GROMACS	is  a full-featured suite of programs to perform molecular dy-
       namics simulations, i.e., to simulate the behavior of systems with hun-
       dreds 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.

OPTIONS
       Other options:

       -[no]h (no)
	      Print help and quit

       -[no]quiet (no)
	      Do not print common startup info or quotes

       -[no]version (no)
	      Print extended version information and quit

       -[no]copyright (yes)
	      Print copyright information on startup

       -nice <int> (19)
	      Set the nicelevel	(default depends on command)

       -[no]backup (yes)
	      Write backups if output files exist

GMX COMMANDS
       The following commands are available. Please refer to their  individual
       man pages or gmx	help <command> for further details.

   Trajectory analysis
       gmx-gangle(1)
	      Calculate	angles

       gmx-convert-trj(1)
	      Converts between different trajectory types

       gmx-distance(1)
	      Calculate	distances between pairs	of positions

       gmx-extract-cluster(1)
	      Allows  extracting frames	corresponding to clusters from trajec-
	      tory

       gmx-freevolume(1)
	      Calculate	free volume

       gmx-pairdist(1)
	      Calculate	pairwise distances between groups of positions

       gmx-rdf(1)
	      Calculate	radial distribution functions

       gmx-sasa(1)
	      Compute solvent accessible surface area

       gmx-select(1)
	      Print general information	about selections

       gmx-trajectory(1)
	      Print coordinates, velocities, and/or forces for selections

   Generating topologies and coordinates
       gmx-editconf(1)
	      Edit the box and write subgroups

       gmx-x2top(1)
	      Generate a primitive topology from coordinates

       gmx-solvate(1)
	      Solvate a	system

       gmx-insert-molecules(1)
	      Insert molecules into existing vacancies

       gmx-genconf(1)
	      Multiply a conformation in arandoma orientations

       gmx-genion(1)
	      Generate monoatomic ions on energetically	favorable positions

       gmx-genrestr(1)
	      Generate position	restraints or distance	restraints  for	 index
	      groups

       gmx-pdb2gmx(1)
	      Convert coordinate files to topology and FF-compliant coordinate
	      files

   Running a simulation
       gmx-grompp(1)
	      Make a run input file

       gmx-mdrun(1)
	      Perform a	simulation, do a normal	mode  analysis	or  an	energy
	      minimization

       gmx-convert-tpr(1)
	      Make a modifed run-input file

   Viewing trajectories
       gmx-nmtraj(1)
	      Generate a virtual oscillating trajectory	from an	eigenvector

       gmx-view(1)
	      View a trajectory	on an X-Windows	terminal

   Processing energies
       gmx-enemat(1)
	      Extract an energy	matrix from an energy file

       gmx-energy(1)
	      Writes energies to xvg files and display averages

       gmx-mdrun(1)
	      (Re)calculate energies for trajectory frames with	-rerun

   Converting files
       gmx-editconf(1)
	      Convert and manipulates structure	files

       gmx-eneconv(1)
	      Convert energy files

       gmx-sigeps(1)
	      Convert c6/12 or c6/cn combinations to and from sigma/epsilon

       gmx-trjcat(1)
	      Concatenate trajectory files

       gmx-trjconv(1)
	      Convert and manipulates trajectory files

       gmx-xpm2ps(1)
	      Convert XPM (XPixelMap) matrices to postscript or	XPM

   Tools
       gmx-analyze(1)
	      Analyze data sets

       gmx-awh(1)
	      Extract data from	an accelerated weight histogram	(AWH) run

       gmx-filter(1)
	      Frequency	filter trajectories, useful for	making smooth movies

       gmx-lie(1)
	      Estimate free energy from	linear combinations

       gmx-pme_error(1)
	      Estimate the error of using PME with a given input file

       gmx-sham(1)
	      Compute free energies or other histograms	from histograms

       gmx-spatial(1)
	      Calculate	the spatial distribution function

       gmx-traj(1)
	      Plot  x,	v, f, box, temperature and rotational energy from tra-
	      jectories

       gmx-tune_pme(1)
	      Time mdrun as a function of PME ranks to optimize	settings

       gmx-wham(1)
	      Perform weighted histogram analysis after	umbrella sampling

       gmx-check(1)
	      Check and	compare	files

       gmx-dump(1)
	      Make binary files	human readable

       gmx-make_ndx(1)
	      Make index files

       gmx-mk_angndx(1)
	      Generate index files for agmx anglea

       gmx-trjorder(1)
	      Order molecules according	to their distance to a group

       gmx-xpm2ps(1)
	      Convert XPM (XPixelMap) matrices to postscript or	XPM

       gmx-report-methods(1)
	      Write short summary about	the simulation setup to	 a  text  file
	      and/or to	the standard output.

   Distances between structures
       gmx-cluster(1)
	      Cluster structures

       gmx-confrms(1)
	      Fit two structures and calculates	the RMSD

       gmx-rms(1)
	      Calculate	RMSDs with a reference structure and RMSD matrices

       gmx-rmsf(1)
	      Calculate	atomic fluctuations

   Distances in	structures over	time
       gmx-mindist(1)
	      Calculate	the minimum distance between two groups

       gmx-mdmat(1)
	      Calculate	residue	contact	maps

       gmx-polystat(1)
	      Calculate	static properties of polymers

       gmx-rmsdist(1)
	      Calculate	atom pair distances averaged with power	-2, -3 or -6

   Mass	distribution properties	over time
       gmx-gyrate(1)
	      Calculate	the radius of gyration

       gmx-msd(1)
	      Calculates mean square displacements

       gmx-polystat(1)
	      Calculate	static properties of polymers

       gmx-rdf(1)
	      Calculate	radial distribution functions

       gmx-rotacf(1)
	      Calculate	the rotational correlation function for	molecules

       gmx-rotmat(1)
	      Plot the rotation	matrix for fitting to a	reference structure

       gmx-sans(1)
	      Compute small angle neutron scattering spectra

       gmx-saxs(1)
	      Compute small angle X-ray	scattering spectra

       gmx-traj(1)
	      Plot  x,	v, f, box, temperature and rotational energy from tra-
	      jectories

       gmx-vanhove(1)
	      Compute Van Hove displacement and	correlation functions

   Analyzing bonded interactions
       gmx-angle(1)
	      Calculate	distributions and correlations for  angles  and	 dihe-
	      drals

       gmx-mk_angndx(1)
	      Generate index files for agmx anglea

   Structural properties
       gmx-bundle(1)
	      Analyze bundles of axes, e.g., helices

       gmx-clustsize(1)
	      Calculate	size distributions of atomic clusters

       gmx-disre(1)
	      Analyze distance restraints

       gmx-hbond(1)
	      Compute and analyze hydrogen bonds

       gmx-order(1)
	      Compute the order	parameter per atom for carbon tails

       gmx-principal(1)
	      Calculate	principal axes of inertia for a	group of atoms

       gmx-rdf(1)
	      Calculate	radial distribution functions

       gmx-saltbr(1)
	      Compute salt bridges

       gmx-sorient(1)
	      Analyze solvent orientation around solutes

       gmx-spol(1)
	      Analyze  solvent	dipole	orientation  and  polarization	around
	      solutes

   Kinetic properties
       gmx-bar(1)
	      Calculate	free energy difference estimates through Bennettas ac-
	      ceptance ratio

       gmx-current(1)
	      Calculate	dielectric constants and current autocorrelation func-
	      tion

       gmx-dos(1)
	      Analyze density of states	and properties based on	that

       gmx-dyecoupl(1)
	      Extract dye dynamics from	trajectories

       gmx-principal(1)
	      Calculate	principal axes of inertia for a	group of atoms

       gmx-tcaf(1)
	      Calculate	viscosities of liquids

       gmx-traj(1)
	      Plot x, v, f, box, temperature and rotational energy  from  tra-
	      jectories

       gmx-vanhove(1)
	      Compute Van Hove displacement and	correlation functions

       gmx-velacc(1)
	      Calculate	velocity autocorrelation functions

   Electrostatic properties
       gmx-current(1)
	      Calculate	dielectric constants and current autocorrelation func-
	      tion

       gmx-dielectric(1)
	      Calculate	frequency dependent dielectric constants

       gmx-dipoles(1)
	      Compute the total	dipole plus fluctuations

       gmx-potential(1)
	      Calculate	the electrostatic potential across the box

       gmx-spol(1)
	      Analyze  solvent	dipole	orientation  and  polarization	around
	      solutes

       gmx-genion(1)
	      Generate monoatomic ions on energetically	favorable positions

   Protein-specific analysis
       gmx-do_dssp(1)
	      Assign secondary structure and calculate solvent accessible sur-
	      face area

       gmx-chi(1)
	      Calculate	everything you want to know about chi and other	 dihe-
	      drals

       gmx-helix(1)
	      Calculate	basic properties of alpha helices

       gmx-helixorient(1)
	      Calculate	 local	pitch/bending/rotation/orientation  inside he-
	      lices

       gmx-rama(1)
	      Compute Ramachandran plots

       gmx-wheel(1)
	      Plot helical wheels

   Interfaces
       gmx-bundle(1)
	      Analyze bundles of axes, e.g., helices

       gmx-density(1)
	      Calculate	the density of the system

       gmx-densmap(1)
	      Calculate	2D planar or axial-radial density maps

       gmx-densorder(1)
	      Calculate	surface	fluctuations

       gmx-h2order(1)
	      Compute the orientation of water molecules

       gmx-hydorder(1)
	      Compute tetrahedrality parameters	around a given atom

       gmx-order(1)
	      Compute the order	parameter per atom for carbon tails

       gmx-potential(1)
	      Calculate	the electrostatic potential across the box

   Covariance analysis
       gmx-anaeig(1)
	      Analyze the eigenvectors

       gmx-covar(1)
	      Calculate	and diagonalize	the covariance matrix

       gmx-make_edi(1)
	      Generate input files for essential dynamics sampling

   Normal modes
       gmx-anaeig(1)
	      Analyze the normal modes

       gmx-nmeig(1)
	      Diagonalize the Hessian for normal mode analysis

       gmx-nmtraj(1)
	      Generate a virtual oscillating trajectory	from an	eigenvector

       gmx-nmens(1)
	      Generate an ensemble of structures from the normal modes

       gmx-grompp(1)
	      Make a run input file

       gmx-mdrun(1)
	      Find a potential energy minimum and calculate the	Hessian

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020				GMX(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | GMX COMMANDS | COPYRIGHT

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