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. Trajectory analysis

  gmx-gangle	Calculate angles
  gmx-distance	Calculate distances between pairs of positions
  gmx-freevolume	Calculate free volume
  gmx-sasa	Compute solvent accessible surface area
  gmx-select	Print general information about selections

Generating topologies and coordinates

  gmx-editconf	Edit the box and write subgroups
  gmx-protonate	Protonate structures
  gmx-x2top	Generate a primitive topology from coordinates
  gmx-solvate	Solvate a system
  gmx-insert-molecules	Insert molecules into existing vacancies
  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-pdb2gmx	Convert coordinate files to topology and FF-compliant coordinate files

Running a simulation

  gmx-grompp	Make a run input file
  gmx-mdrun	Perform a simulation, do a normal mode analysis or an energy minimization
  gmx-convert-tpr	Make a modifed run-input file

Viewing trajectories

  gmx-nmtraj	Generate a virtual oscillating trajectory from an eigenvector
  gmx-view	View a trajectory on an X-Windows terminal

Processing energies

  gmx-enemat	Extract an energy matrix from an energy file
  gmx-energy	Writes energies to xvg files and display averages
  gmx-mdrun	(Re)calculate energies for trajectory frames with -rerun

Converting files

  gmx-editconf	Convert and manipulates structure files
  gmx-eneconv	Convert energy files
  gmx-sigeps	Convert c6/12 or c6/cn combinations to and from sigma/epsilon
  gmx-trjcat	Concatenate trajectory files
  gmx-trjconv	Convert and manipulates trajectory files
  gmx-xpm2ps	Convert XPM (XPixelMap) matrices to postscript or XPM

Tools

  gmx-analyze	Analyze data sets
  gmx-dyndom	Interpolate and extrapolate structure rotations
  gmx-filter	Frequency filter trajectories, useful for making smooth movies
  gmx-lie	Estimate free energy from linear combinations
  gmx-morph	Interpolate linearly between conformations
  gmx-pme_error	Estimate the error of using PME with a given input file
  gmx-sham	Compute free energies or other histograms from histograms
  gmx-spatial	Calculate the spatial distribution function
  gmx-traj	Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-tune_pme	Time mdrun as a function of PME ranks to optimize settings
  gmx-wham	Perform weighted histogram analysis after umbrella sampling
  gmx-check	Check and compare files
  gmx-dump	Make binary files human readable
  gmx-make_ndx	Make index files
  gmx-mk_angndx	Generate index files for 'gmx angle'
  gmx-trjorder	Order molecules according to their distance to a group
  gmx-xpm2ps	Convert XPM (XPixelMap) matrices to postscript or XPM

Distances between structures

  gmx-cluster	Cluster structures
  gmx-confrms	Fit two structures and calculates the RMSD
  gmx-rms	Calculate RMSDs with a reference structure and RMSD matrices
  gmx-rmsf	Calculate atomic fluctuations

Distances in structures over time

  gmx-mindist	Calculate the minimum distance between two groups
  gmx-mdmat	Calculate residue contact maps
  gmx-polystat	Calculate static properties of polymers
  gmx-rmsdist	Calculate atom pair distances averaged with power -2, -3 or -6

Mass distribution properties over time

  gmx-gyrate	Calculate the radius of gyration
  gmx-msd	Calculates mean square displacements
  gmx-polystat	Calculate static properties of polymers
  gmx-rdf	Calculate radial distribution functions
  gmx-rotacf	Calculate the rotational correlation function for molecules
  gmx-rotmat	Plot the rotation matrix for fitting to a reference structure
  gmx-sans	Compute small angle neutron scattering spectra
  gmx-saxs	Compute small angle X-ray scattering spectra
  gmx-traj	Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-vanhove	Compute Van Hove displacement and correlation functions

Analyzing bonded interactions

  gmx-angle	Calculate distributions and correlations for angles and dihedrals
  gmx-mk_angndx	Generate index files for 'gmx angle'

Structural properties

  gmx-anadock	Cluster structures from Autodock runs
  gmx-bundle	Analyze bundles of axes, e.g., helices
  gmx-clustsize	Calculate size distributions of atomic clusters
  gmx-disre	Analyze distance restraints
  gmx-hbond	Compute and analyze hydrogen bonds
  gmx-order	Compute the order parameter per atom for carbon tails
  gmx-principal	Calculate principal axes of inertia for a group of atoms
  gmx-rdf	Calculate radial distribution functions
  gmx-saltbr	Compute salt bridges
  gmx-sorient	Analyze solvent orientation around solutes
  gmx-spol	Analyze solvent dipole orientation and polarization around solutes

Kinetic properties

  gmx-bar	Calculate free energy difference estimates through Bennett's acceptance ratio
  gmx-current	Calculate dielectric constants and current autocorrelation function
  gmx-dos	Analyze density of states and properties based on that
  gmx-dyecoupl	Extract dye dynamics from trajectories
  gmx-principal	Calculate principal axes of inertia for a group of atoms
  gmx-tcaf	Calculate viscosities of liquids
  gmx-traj	Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-vanhove	Compute Van Hove displacement and correlation functions
  gmx-velacc	Calculate velocity autocorrelation functions

Electrostatic properties

  gmx-current	Calculate dielectric constants and current autocorrelation function
  gmx-dielectric	Calculate frequency dependent dielectric constants
  gmx-dipoles	Compute the total dipole plus fluctuations
  gmx-potential	Calculate the electrostatic potential across the box
  gmx-spol	Analyze solvent dipole orientation and polarization around solutes
  gmx-genion	Generate monoatomic ions on energetically favorable positions

Protein-specific analysis

  gmx-do_dssp	Assign secondary structure and calculate solvent accessible surface area
  gmx-chi	Calculate everything you want to know about chi and other dihedrals
  gmx-helix	Calculate basic properties of alpha helices
  gmx-helixorient	Calculate local pitch/bending/rotation/orientation inside helices
  gmx-rama	Compute Ramachandran plots
  gmx-wheel	Plot helical wheels

Interfaces

  gmx-bundle	Analyze bundles of axes, e.g., helices
  gmx-density	Calculate the density of the system
  gmx-densmap	Calculate 2D planar or axial-radial density maps
  gmx-densorder	Calculate surface fluctuations
  gmx-h2order	Compute the orientation of water molecules
  gmx-hydorder	Compute tetrahedrality parameters around a given atom
  gmx-order	Compute the order parameter per atom for carbon tails
  gmx-potential	Calculate the electrostatic potential across the box

Covariance analysis

  gmx-anaeig	Analyze the eigenvectors
  gmx-covar	Calculate and diagonalize the covariance matrix
  gmx-make_edi	Generate input files for essential dynamics sampling

Normal modes

  gmx-anaeig	Analyze the normal modes
  gmx-nmeig	Diagonalize the Hessian for normal mode analysis
  gmx-nmtraj	Generate a virtual oscillating trajectory from an eigenvector
  gmx-nmens	Generate an ensemble of structures from the normal modes
  gmx-grompp	Make a run input file
  gmx-mdrun	Find a potential energy minimum and calculate 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 is available in /usr/share/doc/gromacs/html/ .

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.