The following commands are available. Please refer to their individual man pages or gmxhelp<command>
for further details.
Trajectoryanalysisgmx-gangle(1)
Calculate angles
gmx-convert-trj(1)
Converts between different trajectory types
gmx-distance(1)
Calculate distances between pairs of positions
gmx-dssp(1)
Calculate protein secondary structure via DSSP algorithm
gmx-extract-cluster(1)
Allows extracting frames corresponding to clusters from trajectory
gmx-freevolume(1)
Calculate free volume
gmx-hbond(1)
Compute and analyze hydrogen bonds.
gmx-msd(1)
Compute mean squared displacements
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-scattering(1)
Calculate small angle scattering profiles for SANS or SAXS
gmx-select(1)
Print general information about selections
gmx-trajectory(1)
Print coordinates, velocities, and/or forces for selections
gmx-gyrate(1)
Calculate radius of gyration of a molecule
Generatingtopologiesandcoordinatesgmx-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
Runningasimulationgmx-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 modified run-input file
Viewingtrajectoriesgmx-nmtraj(1)
Generate a virtual oscillating trajectory from an eigenvector
Processingenergiesgmx-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
Convertingfilesgmx-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
Toolsgmx-analyze(1)
Analyze data sets
gmx-awh(1)
Extract data from an accelerated weight histogram (AWH) run
gmx-filter(1)
Frequency filter trajectories, useful for making smooth movies
gmx-lie(1)
Estimate free energy from linear combinations
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.
Distancesbetweenstructuresgmx-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
Distancesinstructuresovertimegmx-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
Massdistributionpropertiesovertimegmx-gyrate-legacy(1)
Calculate the radius of gyration
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-legacy(1)
Compute small angle neutron scattering spectra
gmx-saxs-legacy(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
Analyzingbondedinteractionsgmx-angle(1)
Calculate distributions and correlations for angles and dihedrals
gmx-mk_angndx(1)
Generate index files for 'gmx angle'
Structuralpropertiesgmx-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-legacy(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
Kineticpropertiesgmx-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
Electrostaticpropertiesgmx-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-specificanalysisgmx-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
Interfacesgmx-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
Covarianceanalysisgmx-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
Normalmodesgmx-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
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