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