GROMACS Programs by Name

Main Table of Contents VERSION 5.0.1

GROMACS Programs Alphabetically

gmx anadock - Cluster structures from Autodock runs
gmx anaeig - Analyze eigenvectors/normal modes
gmx analyze - Analyze data sets
gmx angle - Calculate distributions and correlations for angles and dihedrals
gmx bar - Calculate free energy difference estimates through Bennett's acceptance ratio
gmx bundle - Analyze bundles of axes, e.g., helices
gmx check - Check and compare files
gmx chi - Calculate everything you want to know about chi and other dihedrals
gmx cluster - Cluster structures
gmx clustsize - Calculate size distributions of atomic clusters
gmx confrms - Fit two structures and calculates the RMSD
gmx convert-tpr - Make a modifed run-input file
gmx covar - Calculate and diagonalize the covariance matrix
gmx current - Calculate dielectric constants and current autocorrelation function
gmx density - Calculate the density of the system
gmx densmap - Calculate 2D planar or axial-radial density maps
gmx densorder - Calculate surface fluctuations
gmx dielectric - Calculate frequency dependent dielectric constants
gmx dipoles - Compute the total dipole plus fluctuations
gmx disre - Analyze distance restraints
gmx distance - Calculate distances between pairs of positions
gmx do_dssp - Assign secondary structure and calculate solvent accessible surface area
gmx dos - Analyze density of states and properties based on that
gmx dump - Make binary files human readable
gmx dyecoupl - Extract dye dynamics from trajectories
gmx dyndom - Interpolate and extrapolate structure rotations
gmx editconf - Convert and manipulates structure files
gmx eneconv - Convert energy files
gmx enemat - Extract an energy matrix from an energy file
gmx energy - Writes energies to xvg files and display averages
gmx filter - Frequency filter trajectories, useful for making smooth movies
gmx freevolume - Calculate free volume
gmx gangle - Calculate angles
gmx genconf - Multiply a conformation in 'random' orientations
gmx genion - Generate monoatomic ions on energetically favorable positions
gmx genrestr - Generate position restraints or distance restraints for index groups
gmx grompp - Make a run input file
gmx gyrate - Calculate the radius of gyration
gmx h2order - Compute the orientation of water molecules
gmx hbond - Compute and analyze hydrogen bonds
gmx helix - Calculate basic properties of alpha helices
gmx helixorient - Calculate local pitch/bending/rotation/orientation inside helices
gmx help - Print help information
gmx hydorder - Compute tetrahedrality parameters around a given atom
gmx insert-molecules - Insert molecules into existing vacancies
gmx lie - Estimate free energy from linear combinations
gmx make_edi - Generate input files for essential dynamics sampling
gmx make_ndx - Make index files
gmx mdmat - Calculate residue contact maps
gmx mdrun - Perform a simulation, do a normal mode analysis or an energy minimization
gmx mindist - Calculate the minimum distance between two groups
gmx mk_angndx - Generate index files for 'gmx angle'
gmx morph - Interpolate linearly between conformations
gmx msd - Calculates mean square displacements
gmx nmeig - Diagonalize the Hessian for normal mode analysis
gmx nmens - Generate an ensemble of structures from the normal modes
gmx nmtraj - Generate a virtual oscillating trajectory from an eigenvector
gmx order - Compute the order parameter per atom for carbon tails
gmx pdb2gmx - Convert coordinate files to topology and FF-compliant coordinate files
gmx pme_error - Estimate the error of using PME with a given input file
gmx polystat - Calculate static properties of polymers
gmx potential - Calculate the electrostatic potential across the box
gmx principal - Calculate principal axes of inertia for a group of atoms
gmx protonate - Protonate structures
gmx rama - Compute Ramachandran plots
gmx rdf - Calculate radial distribution functions
gmx rms - Calculate RMSDs with a reference structure and RMSD matrices
gmx rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6
gmx rmsf - Calculate atomic fluctuations
gmx rotacf - Calculate the rotational correlation function for molecules
gmx rotmat - Plot the rotation matrix for fitting to a reference structure
gmx saltbr - Compute salt bridges
gmx sans - Compute small angle neutron scattering spectra
gmx sasa - Compute solvent accessible surface area
gmx saxs - Compute small angle X-ray scattering spectra
gmx select - Print general information about selections
gmx sham - Compute free energies or other histograms from histograms
gmx sigeps - Convert c6/12 or c6/cn combinations to and from sigma/epsilon
gmx solvate - Solvate a system
gmx sorient - Analyze solvent orientation around solutes
gmx spatial - Calculate the spatial distribution function
gmx spol - Analyze solvent dipole orientation and polarization around solutes
gmx tcaf - Calculate viscosities of liquids
gmx traj - Plot x, v, f, box, temperature and rotational energy from trajectories
gmx trjcat - Concatenate trajectory files
gmx trjconv - Convert and manipulates trajectory files
gmx trjorder - Order molecules according to their distance to a group
gmx tune_pme - Time mdrun as a function of PME ranks to optimize settings
gmx vanhove - Compute Van Hove displacement and correlation functions
gmx velacc - Calculate velocity autocorrelation functions
gmx view - View a trajectory on an X-Windows terminal
gmx wham - Perform weighted histogram analysis after umbrella sampling
gmx wheel - Plot helical wheels
gmx x2top - Generate a primitive topology from coordinates
gmx xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM