GROMACS(7) GROMACS Manual GROMACS(7)NAMEgromacs - molecular dynamics simulation suite
DESCRIPTION
GROMACS (the Groningen Machine for Chemical Simulations) is a full-fea‐
tured suite of programs to perform molecular dynamics simulations - in
other words, to simulate the behavior of systems with hundreds to mil‐
lions of particles, using Newtonian equations of motion. It is primar‐
ily used for research on proteins, lipids, and polymers, but can be
applied to a wide variety of chemical and biological research ques‐
tions.
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-freevolumeCalculate 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-moleculesInsert 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-tprMake 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-dielectricCalculate 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-helixorientCalculate 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 partic‐
ular, 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 mes‐
sage-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 pack‐
age 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 pos‐
sible, please try to reproduce bugs on another machine before reporting
them.
VERSION 5.0.6GROMACS(7)
