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GROMACS(7) GROMACS Manual GROMACS(7)NAMEgromacs - molecular dynamics simulation suiteDESCRIPTIONGROMACS(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 ap- plied to a wide variety of chemical and biological research questions.SYNOPSISThe following commands make up the GROMACS suite. Please refer to their individual man pages for further details.Trajectoryanalysisgmx-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 selectionsGeneratingtopologiesandcoordinatesgmx-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 filesRunningasimulationgmx-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 fileViewingtrajectoriesgmx-nmtraj Generate a virtual oscillating trajectory from an eigenvector gmx-view View a trajectory on an X-Windows terminalProcessingenergiesgmx-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 -rerunConvertingfilesgmx-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 XPMToolsgmx-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 XPMDistancesbetweenstructuresgmx-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 fluctuationsDistancesinstructuresovertimegmx-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 -6Massdistributionpropertiesovertimegmx-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 functionsAnalyzingbondedinteractionsgmx-angle Calculate distributions and correlations for angles and dihedrals gmx-mk_angndx Generate index files for 'gmx angle'Structuralpropertiesgmx-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 solutesKineticpropertiesgmx-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 functionsElectrostaticpropertiesgmx-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 positionsProtein-specificanalysisgmx-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 wheelsInterfacesgmx-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 boxCovarianceanalysisgmx-anaeig Analyze the eigenvectors gmx-covar Calculate and diagonalize the covariance matrix gmx-make_edi Generate input files for essential dynamics samplingNormalmodesgmx-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 HessianADDITIONAL DOCUMENTATIONConsult 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/.REFERENCESThe 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:Ames-sage-passingparallelmoleculardynamicsimplementation. Comp. Phys. Comm.91, 43-56 (1995) Erik Lindahl, Berk Hess and David van der Spoel.GROMACS3.0:Apack-ageformolecularsimulationandtrajectoryanalysis. J. Mol. Mod.7, 306-317 (2001) B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl.GROMACS4:Al-gorithmsforHighlyEfficient,Load-Balanced,andScalableMolecularSimulation. J. Chem. Theory Comput.4, 3, 435-447 (2008), <http://dx.doi.org/10.1021/ct700301q>AUTHORSCurrent 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>.BUGSGROMACS 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 5.0.6 GROMACS(7)

NAME | DESCRIPTION | SYNOPSIS | ADDITIONAL DOCUMENTATION | REFERENCES | AUTHORS | BUGS

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