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