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
