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 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.