Molecular dynamics simulation suite

**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.

The following commands make up the GROMACS suite. Please refer to their individual man pages for further details.

**\$1**

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

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 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 gmx-nmtraj Generate a virtual oscillating trajectory from an eigenvector gmx-view View a trajectory on an X-Windows terminal 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 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 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 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 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 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 gmx-angle Calculate distributions and correlations for angles and dihedrals gmx-mk_angndx Generate index files for 'gmx angle' 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 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 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 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 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 gmx-anaeig Analyze the eigenvectors gmx-covar Calculate and diagonalize the covariance matrix gmx-make_edi Generate input files for essential dynamics sampling 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

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/** .

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*>

Current developers:

David van der Spoel <[email protected]>

Berk Hess <[email protected]>

Erik Lindahl <[email protected]>

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 <[email protected]>.

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.