Gromacs-Data

• demux(1) Convert XPLOR distance restraints to Gromacs format
• gmx_d(1) molecular dynamics simulation suite
• gmx_mpi_d(1) molecular dynamics simulation suite
• gmx_mpi(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 modifed 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-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-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 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-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(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(1) molecular dynamics simulation suite
• xplor2gmx(1) Convert XPLOR distance restraints to Gromacs format