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 dynamics simulations,
       i.e., 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.

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-distance(1)
              Calculate distances between pairs of positions

       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

   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 'random' 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-dyndom(1)
              Interpolate and extrapolate structure rotations

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

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

       gmx-morph(1)
              Interpolate linearly between conformations

       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 trajectories

       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 'gmx angle'

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

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

   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 trajectories

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

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

       gmx-mk_angndx(1)
              Generate index files for 'gmx angle'

   Structural properties
       gmx-anadock(1)
              Cluster structures from Autodock runs

       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 Bennett's acceptance ratio

       gmx-current(1)
              Calculate dielectric constants and current autocorrelation function

       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 trajectories

       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 function

       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 surface area

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

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

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

       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

       2015, GROMACS development team