Provided by: gromacs-data_4.6.5-1build1_all 
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
editconf edits the box and writes subgroups
g_protonate protonates structures
g_x2top generates a primitive topology from coordinates
genbox solvates a system
genconf multiplies a conformation in 'random' orientations
genion generates mono atomic ions on energetically favorable positions
genrestr generates position restraints or distance restraints for index groups
pdb2gmx converts coordinate files to topology and FF-compliant coordinate files
Running a simulation
grompp makes a run input file
mdrun performs a simulation, do a normal mode analysis or an energy minimization
tpbconv makes a run input file for restarting a crashed run
Viewing trajectories
g_nmtraj generate a virtual trajectory from an eigenvector
ngmx displays a trajectory
Processing energies
g_enemat extracts an energy matrix from an energy file
g_energy writes energies to xvg files and displays averages
mdrun with -rerun (re)calculates energies for trajectory frames
Converting files
editconf converts and manipulates structure files
eneconv converts energy files
g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon
trjcat concatenates trajectory files
trjconv converts and manipulates trajectory files
xpm2ps converts XPM matrices to encapsulated postscript (or XPM)
Tools
g_analyze analyzes data sets
g_dyndom interpolate and extrapolate structure rotations
g_filter frequency filters trajectories, useful for making smooth movies
g_lie free energy estimate from linear combinations
g_morph linear interpolation of conformations
g_pme_error estimates the error of using PME with a given input file
g_select selects groups of atoms based on flexible textual selections
g_sham read/write xmgr and xvgr data sets
g_spatial calculates the spatial distribution function
g_traj plots x, v and f of selected atoms/groups (and more) from a trajectory
g_tune_pme time mdrun as a function of PME nodes to optimize settings
g_wham weighted histogram analysis after umbrella sampling
gmxcheck checks and compares files
gmxdump makes binary files human readable
make_ndx makes index files
mk_angndx generates index files for g_angle
trjorder orders molecules according to their distance to a group
xpm2ps convert XPM (XPixelMap) file to postscript
Distances between structures
g_cluster clusters structures
g_confrms fits two structures and calculates the rmsd
g_rms calculates rmsd's with a reference structure and rmsd matrices
g_rmsf calculates atomic fluctuations
Distances in structures over time
g_bond calculates distances between atoms
g_dist calculates the distances between the centers of mass of two groups
g_mindist calculates the minimum distance between two groups
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_gyrate calculates the radius of gyration
g_msd calculates mean square displacements
g_polystat calculates static properties of polymers
g_rdf calculates radial distribution functions
g_rotacf calculates the rotational correlation function for molecules
g_rotmat plots the rotation matrix for fitting to a reference structure
g_sans computes the small angle neutron scattering spectra
g_traj plots x, v, f, box, temperature and rotational energy
g_vanhove calculates Van Hove displacement functions
Analyzing bonded interactions
g_angle calculates distributions and correlations for angles and dihedrals
g_bond calculates bond length distributions
mk_angndx generates index files for g_angle
Structural properties
g_anadock cluster structures from Autodock runs
g_bundle analyzes bundles of axes, e.g. helices
g_clustsize calculate size distributions of atomic clusters
g_disre analyzes distance restraints
g_hbond computes and analyzes hydrogen bonds
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_saltbr computes salt bridges
g_sas computes solvent accessible surface area
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
Kinetic properties
g_bar calculates free energy difference estimates through Bennett's acceptance ratio
g_current calculate current autocorrelation function of system
g_dos analyzes density of states and properties based on that
g_dyecoupl extracts dye dynamics from trajectories
g_kinetics analyzes kinetic constants from properties based on the Eyring model
g_principal calculate principal axes of inertion for a group of atoms
g_tcaf calculates viscosities of liquids
g_traj plots x, v, f, box, temperature and rotational energy
g_vanhove compute Van Hove correlation function
g_velacc calculates velocity autocorrelation functions
Electrostatic properties
g_current calculates dielectric constants for charged systems
g_dielectric calculates frequency dependent dielectric constants
g_dipoles computes the total dipole plus fluctuations
g_potential calculates the electrostatic potential across the box
g_spol analyze dipoles around a solute
genion generates mono atomic ions on energetically favorable positions
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 basic properties of alpha helices
g_helixorient calculates local pitch/bending/rotation/orientation inside helices
g_rama computes Ramachandran plots
g_wheel plots helical wheels
g_xrama shows animated Ramachandran plots
Interfaces
g_bundle analyzes bundles of axes, e.g. transmembrane helices
g_density calculates the density of the system
g_densmap calculates 2D planar or axial-radial density maps
g_densorder calculate surface fluctuations
g_h2order computes the orientation of water molecules
g_hydorder computes tetrahedrality parameters around a given atom
g_order computes the order parameter per atom for carbon tails
g_membed embeds a protein into a lipid bilayer
g_potential calculates the electrostatic potential across the box
Covariance analysis
g_anaeig analyzes the eigenvectors
g_covar calculates and diagonalizes the covariance matrix
make_edi generate input files for essential dynamics sampling
Normal modes
g_anaeig analyzes the normal modes
g_nmeig diagonalizes the Hessian
g_nmtraj generate oscillating trajectory of an eigenmode
g_nmens generates an ensemble of structures from the normal modes
grompp makes a run input file
mdrun finds a potential energy minimum and calculates the Hessian
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 particular, 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 reporting them.