GROMACS Programs by Topic

Main Table of Contents VERSION 5.0.4

GROMACS Programs by Topic

Trajectory analysis

gmx gangle - Calculate angles
gmx distance - Calculate distances between pairs of positions
gmx freevolume - Calculate free volume
gmx sasa - Compute solvent accessible surface area
gmx select - Print general information about selections

Generating topologies and coordinates

gmx editconf - Edit the box and write subgroups
gmx protonate - Protonate structures
gmx x2top - Generate a primitive topology from coordinates
gmx solvate - Solvate a system
gmx insert-molecules - Insert molecules into existing vacancies
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 pdb2gmx - Convert coordinate files to topology and FF-compliant coordinate files

Running a simulation

gmx grompp - Make a run input file
gmx mdrun - Perform a simulation, do a normal mode analysis or an energy minimization
gmx convert-tpr - Make a modifed run-input file

Viewing trajectories

gmx nmtraj - Generate a virtual oscillating trajectory from an eigenvector
gmx view - View a trajectory on an X-Windows terminal

Processing energies

gmx enemat - Extract an energy matrix from an energy file
gmx energy - Writes energies to xvg files and display averages
gmx mdrun - (Re)calculate energies for trajectory frames with -rerun

Converting files

gmx editconf - Convert and manipulates structure files
gmx eneconv - Convert energy files
gmx sigeps - Convert c6/12 or c6/cn combinations to and from sigma/epsilon
gmx trjcat - Concatenate trajectory files
gmx trjconv - Convert and manipulates trajectory files
gmx xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM

Tools

gmx analyze - Analyze data sets
gmx dyndom - Interpolate and extrapolate structure rotations
gmx filter - Frequency filter trajectories, useful for making smooth movies
gmx lie - Estimate free energy from linear combinations
gmx morph - Interpolate linearly between conformations
gmx pme_error - Estimate the error of using PME with a given input file
gmx sham - Compute free energies or other histograms from histograms
gmx spatial - Calculate the spatial distribution function
gmx traj - Plot x, v, f, box, temperature and rotational energy from trajectories
gmx tune_pme - Time mdrun as a function of PME ranks to optimize settings
gmx wham - Perform weighted histogram analysis after umbrella sampling
gmx check - Check and compare files
gmx dump - Make binary files human readable
gmx make_ndx - Make index files
gmx mk_angndx - Generate index files for 'gmx angle'
gmx trjorder - Order molecules according to their distance to a group
gmx xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM

Distances between structures

gmx cluster - Cluster structures
gmx confrms - Fit two structures and calculates the RMSD
gmx rms - Calculate RMSDs with a reference structure and RMSD matrices
gmx rmsf - Calculate atomic fluctuations

Distances in structures over time

gmx mindist - Calculate the minimum distance between two groups
gmx mdmat - Calculate residue contact maps
gmx polystat - Calculate static properties of polymers
gmx rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6

Mass distribution properties over time

gmx gyrate - Calculate the radius of gyration
gmx msd - Calculates mean square displacements
gmx polystat - Calculate static properties of polymers
gmx rdf - Calculate radial distribution functions
gmx rotacf - Calculate the rotational correlation function for molecules
gmx rotmat - Plot the rotation matrix for fitting to a reference structure
gmx sans - Compute small angle neutron scattering spectra
gmx saxs - Compute small angle X-ray scattering spectra
gmx traj - Plot x, v, f, box, temperature and rotational energy from trajectories
gmx vanhove - Compute Van Hove displacement and correlation functions

Analyzing bonded interactions

gmx angle - Calculate distributions and correlations for angles and dihedrals
gmx mk_angndx - Generate index files for 'gmx angle'

Structural properties

gmx anadock - Cluster structures from Autodock runs
gmx bundle - Analyze bundles of axes, e.g., helices
gmx clustsize - Calculate size distributions of atomic clusters
gmx disre - Analyze distance restraints
gmx hbond - Compute and analyze hydrogen bonds
gmx order - Compute the order parameter per atom for carbon tails
gmx principal - Calculate principal axes of inertia for a group of atoms
gmx rdf - Calculate radial distribution functions
gmx saltbr - Compute salt bridges
gmx sorient - Analyze solvent orientation around solutes
gmx spol - Analyze solvent dipole orientation and polarization around solutes

Kinetic properties

gmx bar - Calculate free energy difference estimates through Bennett's acceptance ratio
gmx current - Calculate dielectric constants and current autocorrelation function
gmx dos - Analyze density of states and properties based on that
gmx dyecoupl - Extract dye dynamics from trajectories
gmx principal - Calculate principal axes of inertia for a group of atoms
gmx tcaf - Calculate viscosities of liquids
gmx traj - Plot x, v, f, box, temperature and rotational energy from trajectories
gmx vanhove - Compute Van Hove displacement and correlation functions
gmx velacc - Calculate velocity autocorrelation functions

Electrostatic properties

gmx current - Calculate dielectric constants and current autocorrelation function
gmx dielectric - Calculate frequency dependent dielectric constants
gmx dipoles - Compute the total dipole plus fluctuations
gmx potential - Calculate the electrostatic potential across the box
gmx spol - Analyze solvent dipole orientation and polarization around solutes
gmx genion - Generate monoatomic ions on energetically favorable positions

Protein-specific analysis

gmx do_dssp - Assign secondary structure and calculate solvent accessible surface area
gmx chi - Calculate everything you want to know about chi and other dihedrals
gmx helix - Calculate basic properties of alpha helices
gmx helixorient - Calculate local pitch/bending/rotation/orientation inside helices
gmx rama - Compute Ramachandran plots
gmx wheel - Plot helical wheels

Interfaces

gmx bundle - Analyze bundles of axes, e.g., helices
gmx density - Calculate the density of the system
gmx densmap - Calculate 2D planar or axial-radial density maps
gmx densorder - Calculate surface fluctuations
gmx h2order - Compute the orientation of water molecules
gmx hydorder - Compute tetrahedrality parameters around a given atom
gmx order - Compute the order parameter per atom for carbon tails
gmx potential - Calculate the electrostatic potential across the box

Covariance analysis

gmx anaeig - Analyze the eigenvectors
gmx covar - Calculate and diagonalize the covariance matrix
gmx make_edi - Generate input files for essential dynamics sampling

Normal modes

gmx anaeig - Analyze the normal modes
gmx nmeig - Diagonalize the Hessian for normal mode analysis
gmx nmtraj - Generate a virtual oscillating trajectory from an eigenvector
gmx nmens - Generate an ensemble of structures from the normal modes
gmx grompp - Make a run input file
gmx mdrun - Find a potential energy minimum and calculate the Hessian


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