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