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
  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.