📦 gromacs-common

G

• gmx(1)molecular dynamics simulation suite✨
• 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 modified run-input file✨
• gmx-convert-trj(1)Converts between different trajectory types✨
• 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-dos(1)Analyze density of states and properties based on that✨
• gmx-dssp(1)Calculate protein secondary structure via DSSP algorithm✨
• gmx-dump(1)Make binary files human readable✨
• gmx-dyecoupl(1)Extract dye dynamics from trajectories✨
• 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-extract-cluster(1)Allows extracting frames corresponding to clusters from trajectory✨
• 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 radius of gyration of a molecule✨
• gmx-gyrate-legacy(1)Calculate the radius of gyration✨
• gmx-h2order(1)Compute the orientation of water molecules✨
• gmx-hbond(1)Compute and analyze hydrogen bonds.✨
• gmx-hbond-legacy(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-msd(1)Compute mean squared 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-nonbonded-benchmark(1)Benchmarking tool for the non-bonded pair kernels.✨
• 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-report-methods(1)Write short summary about the simulation setup to a text file and/or to the standard output.✨
• 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-legacy(1)Compute small angle neutron scattering spectra✨
• gmx-sasa(1)Compute solvent accessible surface area✨
• gmx-saxs-legacy(1)Compute small angle X-ray scattering spectra✨
• gmx-scattering(1)Calculate small angle scattering profiles for SANS or SAXS✨
• 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-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✨