GROMACS(7) GROMACS suite, Version 4.0 GROMACS(7)
NAME
gromacs - molecular dynamics simulation suite
DESCRIPTION
GROMACS (the Groningen Machine for Chemical Simulations) is a full-featured suite of programs to perform molecular dynamics simulations -
in other words, to simulate the behavior of systems with hundreds to millions of particles, using Newtonian equations of motion. It is
primarily used for research on proteins, lipids, and polymers, but can be applied to a wide variety of chemical and biological research
questions.
SYNOPSIS
The following commands make up the GROMACS suite. Please refer to their individual man pages for further details.
Generating topologies and coordinates
pdb2gmx converts pdb files to topology and coordinate files
g_x2top generates a primitive topology from coordinates
editconf edits the box and writes subgroups
genbox solvates a system
genion generates mono atomic ions on energetically favorable positions
genconf multiplies a conformation in 'random' orientations
g_protonate protonates structures
Running a simulation
grompp makes a run input file
tpbconv makes a run input file for restarting a crashed run
mdrun performs a simulation, do a normal mode analysis or an energy minimization
mdrun_mpi performs a sim across multiple CPUs or systems
Viewing trajectories
ngmx displays a trajectory
g_highway X Window System gadget for highway simulations
g_nmtraj generate a virtual trajectory from an eigenvector
Processing energies
g_energy writes energies to xvg files and displays averages
g_enemat extracts an energy matrix from an energy file
mdrun with -rerun (re)calculates energies for trajectory frames
Converting files
editconf converts and manipulates structure files
trjconv converts and manipulates trajectory files
trjcat concatenates trajectory files
eneconv converts energy files
xpm2ps converts XPM matrices to encapsulated postscript (or XPM)
g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon
Tools
make_ndx makes index files
mk_angndx generates index files for g_angle
gmxcheck checks and compares files
gmxdump makes binary files human readable
g_traj plots x, v and f of selected atoms/groups (and more) from a trajectory
g_analyze analyzes data sets
trjorder orders molecules according to their distance to a group
g_filter frequency filters trajectories, useful for making smooth movies
g_lie free energy estimate from linear combinations
g_dyndom interpolate and extrapolate structure rotations
g_morph linear interpolation of conformations
g_wham weighted histogram analysis after umbrella sampling
xpm2ps convert XPM (XPixelMap) file to postscript
g_sham read/write xmgr and xvgr data sets
g_spatial calculates the spatial distribution function (more control than g_sdf)
g_sdf calculates the spatial distribution function (faster than g_spatial)
g_select selects groups of atoms based on flexible textual selections
g_tune_pme time mdrun as a function of PME nodes to optimize settings
Distances between structures
g_rms calculates rmsd's with a reference structure and rmsd matrices
g_confrms fits two structures and calculates the rmsd
g_cluster clusters structures
g_rmsf calculates atomic fluctuations
Distances in structures over time
g_mindist calculates the minimum distance between two groups
g_dist calculates the distances between the centers of mass of two groups
g_bond calculates distances between atoms
g_mdmat calculates residue contact maps
g_polystat calculates static properties of polymers
g_rmsdist calculates atom pair distances averaged with power -2, -3 or -6
Mass distribution properties over time
g_traj plots x, v, f, box, temperature and rotational energy
g_gyrate calculates the radius of gyration
g_msd calculates mean square displacements
g_polystat calculates static properties of polymers
g_rotacf calculates the rotational correlation function for molecules
g_rdf calculates radial distribution functions
g_rotmat plots the rotation matrix for fitting to a reference structure
g_vanhove calculates Van Hove displacement functions
Analyzing bonded interactions
g_bond calculates bond length distributions
mk_angndx generates index files for g_angle
g_angle calculates distributions and correlations for angles and dihedrals
g_dih analyzes dihedral transitions
Structural properties
g_hbond computes and analyzes hydrogen bonds
g_saltbr computes salt bridges
g_sas computes solvent accessible surface area
g_order computes the order parameter per atom for carbon tails
g_principal calculates axes of inertia for a group of atoms
g_rdf calculates radial distribution functions
g_sdf calculates solvent distribution functions
g_sgangle computes the angle and distance between two groups
g_sorient analyzes solvent orientation around solutes
g_spol analyzes solvent dipole orientation and polarization around solutes
g_bundle analyzes bundles of axes, e.g. helices
g_disre analyzes distance restraints
g_clustsize calculate size distributions of atomic clusters
g_anadock cluster structures from Autodock runs
Kinetic properties
g_traj plots x, v, f, box, temperature and rotational energy
g_velacc calculates velocity autocorrelation functions
g_tcaf calculates viscosities of liquids
g_kinetics calculate kinetic rate constants (experimental)
g_bar calculates free energy difference estimates through Bennett's acceptance ratio
g_current calculate current autocorrelation function of system
g_vanhove compute Van Hove correlation function
g_principal calculate principal axes of inertion for a group of atoms
Electrostatic properties
genion generates mono atomic ions on energetically favorable positions
g_potential calculates the electrostatic potential across the box
g_dipoles computes the total dipole plus fluctuations
g_dielectric calculates frequency dependent dielectric constants
g_current calculate current autocorrelation function of system
g_spol analyze dipoles around a solute
Protein specific analysis
do_dssp assigns secondary structure and calculates solvent accessible surface area
g_chi calculates everything you want to know about chi and other dihedrals
g_helix calculates everything you want to know about helices
g_helixorient calculate coordinates/directions of alpha-helix components
g_rama computes Ramachandran plots
g_xrama shows animated Ramachandran plots
wheel plots helical wheels
Interfaces
g_potential calculates the electrostatic potential across the box
g_density calculates the density of the system
g_order computes the order parameter per atom for carbon tails
g_h2order computes the orientation of water molecules
g_bundle analyzes bundles of axes, e.g. transmembrane helices
g_membed embeds a protein into a lipid bilayer
Covariance analysis
g_covar calculates and diagonalizes the covariance matrix
g_anaeig analyzes the eigenvectors
make_edi generate essential-dynamics input file from g_covar output
Normal modes
grompp makes a run input file
mdrun finds a potential energy minimum
mdrun calculates the Hessian
g_nmeig diagonalizes the Hessian
make_edi generates essential-dynamics input file from g_nmeig analysis
g_anaeig analyzes the normal modes
g_nmens generates an ensemble of structures from the normal modes
ADDITIONAL DOCUMENTATION
Consult the manual at <http://www.gromacs.org/content/view/27/42/> for an introduction to molecular dynamics in general and GROMACS in par-
ticular, as well as an overview of the individual programs.
The shorter HTML reference and GROMACS FAQ are available in /usr/share/doc/gromacs/html/ .
Tutorial files and other miscellaneous references are stored in /usr/share/gromacs/ .
REFERENCES
The development of GROMACS is mainly funded by academic research grants. To help us fund development, the authors humbly ask that you cite
the GROMACS papers:
H.J.C. Berendsen, D. van der Spoel and R. van Drunen. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys.
Comm. 91, 43-56 (1995)
Erik Lindahl, Berk Hess and David van der Spoel. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7,
306-317 (2001)
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular
Simulation. J. Chem. Theory Comput. 4, 3, 435-447 (2008), <http://dx.doi.org/10.1021/ct700301q>
AUTHORS
Current developers:
David van der Spoel <spoel@gromacs.org>
Berk Hess <hess@gromacs.org>
Erik Lindahl <lindahl@gromacs.org>
A full list of present and former contributors is available at <http://www.gromacs.org>
This manual page is largely based on the GROMACS online reference, and was prepared in this format by Nicholas Breen <nbreen@ofb.net>.
BUGS
GROMACS has no major known bugs, but be warned that it stresses your CPU more than most software. Systems with slightly flaky hardware may
prove unreliable while running heavy-duty simulations. If at all possible, please try to reproduce bugs on another machine before report-
ing them.
gromacs 2008-10-12 GROMACS(7)