Manual pages

Origin: 2018.1.

[ Alias ↣ ] Name (section) Brief
gmx(1) Molecular dynamics simulation suite.
gmx-anadock(1) Cluster structures from Autodock runs.
gmx-anaeig(1) Analyze eigenvectors/normal modes.
gmx-analyze(1) Analyze data sets.
gmx-angle(1) Calculate distributions and correlations for angles and dihedrals.
gmx-awh(1) Extract data from an accelerated weight histogram (AWH) run.
gmx-bar(1) Calculate free energy difference estimates through Bennett's acceptance ratio.
gmx-bundle(1) Analyze bundles of axes, e.g., helices.
gmx-check(1) Check and compare files.
gmx-chi(1) Calculate everything you want to know about chi and other dihedrals.
gmx-cluster(1) Cluster structures.
gmx-clustsize(1) Calculate size distributions of atomic clusters.
gmx-confrms(1) Fit two structures and calculates the RMSD.
gmx-convert-tpr(1) Make a modifed run-input file.
gmx-covar(1) Calculate and diagonalize the covariance matrix.
gmx-current(1) Calculate dielectric constants and current autocorrelation function.
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-dielectric(1) Calculate frequency dependent dielectric constants.
gmx-dipoles(1) Compute the total dipole plus fluctuations.
gmx-disre(1) Analyze distance restraints.
gmx-distance(1) Calculate distances between pairs of positions.
gmx-do_dssp(1) Assign secondary structure and calculate solvent accessible surface area.
gmx-dos(1) Analyze density of states and properties based on that.
gmx-dump(1) Make binary files human readable.
gmx-dyecoupl(1) Extract dye dynamics from trajectories.
gmx-dyndom(1) Interpolate and extrapolate structure rotations.
gmx-editconf(1) Convert and manipulates structure files.
gmx-eneconv(1) Convert energy files.
gmx-enemat(1) Extract an energy matrix from an energy file.
gmx-energy(1) Writes energies to xvg files and display averages.
gmx-filter(1) Frequency filter trajectories, useful for making smooth movies.
gmx-freevolume(1) Calculate free volume.
gmx-gangle(1) Calculate angles.
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-grompp(1) Make a run input file.
gmx-gyrate(1) Calculate the radius of gyration.
gmx-h2order(1) Compute the orientation of water molecules.
gmx-hbond(1) Compute and analyze hydrogen bonds.
gmx-helix(1) Calculate basic properties of alpha helices.
gmx-helixorient(1) Calculate local pitch/bending/rotation/orientation inside helices.
gmx-help(1) Print help information.
gmx-hydorder(1) Compute tetrahedrality parameters around a given atom.
gmx-insert-molecules(1) Insert molecules into existing vacancies.
gmx-lie(1) Estimate free energy from linear combinations.
gmx-make_edi(1) Generate input files for essential dynamics sampling.
gmx-make_ndx(1) Make index files.
gmx-mdmat(1) Calculate residue contact maps.
gmx-mdrun(1) Perform a simulation, do a normal mode analysis or an energy minimization.
gmx-mindist(1) Calculate the minimum distance between two groups.
gmx-mk_angndx(1) Generate index files for 'gmx angle'.
gmx-morph(1) Interpolate linearly between conformations.
gmx-msd(1) Calculates mean square displacements.
gmx-nmeig(1) Diagonalize the Hessian for normal mode analysis.
gmx-nmens(1) Generate an ensemble of structures from the normal modes.
gmx-nmr(1) Analyze nuclear magnetic resonance properties from an energy file.
gmx-nmtraj(1) Generate a virtual oscillating trajectory from an eigenvector.
gmx-order(1) Compute the order parameter per atom for carbon tails.
gmx-pairdist(1) Calculate pairwise distances between groups of positions.
gmx-pdb2gmx(1) Convert coordinate files to topology and FF-compliant coordinate files.
gmx-pme_error(1) Estimate the error of using PME with a given input file.
gmx-polystat(1) Calculate static properties of polymers.
gmx-potential(1) Calculate the electrostatic potential across the box.
gmx-principal(1) Calculate principal axes of inertia for a group of atoms.
gmx-rama(1) Compute Ramachandran plots.
gmx-rdf(1) Calculate radial distribution functions.
gmx-rms(1) Calculate RMSDs with a reference structure and RMSD matrices.
gmx-rmsdist(1) Calculate atom pair distances averaged with power -2, -3 or -6.
gmx-rmsf(1) Calculate atomic fluctuations.
gmx-rotacf(1) Calculate the rotational correlation function for molecules.
gmx-rotmat(1) Plot the rotation matrix for fitting to a reference structure.
gmx-saltbr(1) Compute salt bridges.
gmx-sans(1) Compute small angle neutron scattering spectra.
gmx-sasa(1) Compute solvent accessible surface area.
gmx-saxs(1) Compute small angle X-ray scattering spectra.
gmx-select(1) Print general information about selections.
gmx-sham(1) Compute free energies or other histograms from histograms.
gmx-sigeps(1) Convert c6/12 or c6/cn combinations to and from sigma/epsilon.
gmx-solvate(1) Solvate a system.
gmx-sorient(1) Analyze solvent orientation around solutes.
gmx-spatial(1) Calculate the spatial distribution function.
gmx-spol(1) Analyze solvent dipole orientation and polarization around solutes.
gmx-tcaf(1) Calculate viscosities of liquids.
gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from trajectories.
gmx-trajectory(1) Print coordinates, velocities, and/or forces for selections.
gmx-trjcat(1) Concatenate trajectory files.
gmx-trjconv(1) Convert and manipulates trajectory files.
gmx-trjorder(1) Order molecules according to their distance to a group.
gmx-tune_pme(1) Time mdrun as a function of PME ranks to optimize settings.
gmx-vanhove(1) Compute Van Hove displacement and correlation functions.
gmx-velacc(1) Calculate velocity autocorrelation functions.
gmx-view(1) View a trajectory on an X-Windows terminal.
gmx-wham(1) Perform weighted histogram analysis after umbrella sampling.
gmx-wheel(1) Plot helical wheels.
gmx-x2top(1) Generate a primitive topology from coordinates.
gmx-xpm2ps(1) Convert XPM (XPixelMap) matrices to postscript or XPM.
gmx_d(1) ↣ gmx(1) Molecular dynamics simulation suite.
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