Package gromacs-common

GROMACS shared data and documentation

http://www.gromacs.org

GROMACS is a versatile and extremely well optimized package to perform
molecular dynamics computer simulations and subsequent trajectory analysis.
It is developed for bio-molecules like proteins, but the extremely high
performance means it is used also in several other field like polymer chemistry
and solid state physics.

This package includes architecture independent data and HTML documentation.

General Commands
Command Description
gmx molecular dynamics simulation suite
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-pairdist Calculate pairwise distances between groups of positions
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-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