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 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
2016, GROMACS development team
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