Provided by: gromacs-data_2019.3-2_all

**NAME**

gmx - molecular dynamics simulation suite

**SYNOPSIS**

gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice<int>] [-[no]backup]

**DESCRIPTION**

GROMACS is a full-featured suite of programs to perform molecular dynamics simulations, i.e., 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.

**OPTIONS**

Other options:-[no]h(no)Print help and quit-[no]quiet(no)Do not print common startup info or quotes-[no]version(no)Print extended version information and quit-[no]copyright(yes)Print copyright information on startup-nice<int>(19)Set the nicelevel (default depends on command)-[no]backup(yes)Write backups if output files exist

**GMX** **COMMANDS**

The following commands are available. Please refer to their individual man pages orgmxhelp<command>for further details.Trajectoryanalysisgmx-gangle(1)Calculate anglesgmx-distance(1)Calculate distances between pairs of positionsgmx-freevolume(1)Calculate free volumegmx-pairdist(1)Calculate pairwise distances between groups of positionsgmx-rdf(1)Calculate radial distribution functionsgmx-sasa(1)Compute solvent accessible surface areagmx-select(1)Print general information about selectionsgmx-trajectory(1)Print coordinates, velocities, and/or forces for selectionsGeneratingtopologiesandcoordinatesgmx-editconf(1)Edit the box and write subgroupsgmx-x2top(1)Generate a primitive topology from coordinatesgmx-solvate(1)Solvate a systemgmx-insert-molecules(1)Insert molecules into existing vacanciesgmx-genconf(1)Multiply a conformation in ‘random’ orientationsgmx-genion(1)Generate monoatomic ions on energetically favorable positionsgmx-genrestr(1)Generate position restraints or distance restraints for index groupsgmx-pdb2gmx(1)Convert coordinate files to topology and FF-compliant coordinate filesRunningasimulationgmx-grompp(1)Make a run input filegmx-mdrun(1)Perform a simulation, do a normal mode analysis or an energy minimizationgmx-convert-tpr(1)Make a modifed run-input fileViewingtrajectoriesgmx-nmtraj(1)Generate a virtual oscillating trajectory from an eigenvectorgmx-view(1)View a trajectory on an X-Windows terminalProcessingenergiesgmx-enemat(1)Extract an energy matrix from an energy filegmx-energy(1)Writes energies to xvg files and display averagesgmx-mdrun(1)(Re)calculate energies for trajectory frames with -rerunConvertingfilesgmx-editconf(1)Convert and manipulates structure filesgmx-eneconv(1)Convert energy filesgmx-sigeps(1)Convert c6/12 or c6/cn combinations to and from sigma/epsilongmx-trjcat(1)Concatenate trajectory filesgmx-trjconv(1)Convert and manipulates trajectory filesgmx-xpm2ps(1)Convert XPM (XPixelMap) matrices to postscript or XPMToolsgmx-analyze(1)Analyze data setsgmx-awh(1)Extract data from an accelerated weight histogram (AWH) rungmx-dyndom(1)Interpolate and extrapolate structure rotationsgmx-filter(1)Frequency filter trajectories, useful for making smooth moviesgmx-lie(1)Estimate free energy from linear combinationsgmx-morph(1)Interpolate linearly between conformationsgmx-pme_error(1)Estimate the error of using PME with a given input filegmx-sham(1)Compute free energies or other histograms from histogramsgmx-spatial(1)Calculate the spatial distribution functiongmx-traj(1)Plot x, v, f, box, temperature and rotational energy from trajectoriesgmx-tune_pme(1)Time mdrun as a function of PME ranks to optimize settingsgmx-wham(1)Perform weighted histogram analysis after umbrella samplinggmx-check(1)Check and compare filesgmx-dump(1)Make binary files human readablegmx-make_ndx(1)Make index filesgmx-mk_angndx(1)Generate index files for ‘gmx angle’gmx-trjorder(1)Order molecules according to their distance to a groupgmx-xpm2ps(1)Convert XPM (XPixelMap) matrices to postscript or XPMgmx-report-methods(1)Write short summary about the simulation setup to a text file and/or to the standard output.Distancesbetweenstructuresgmx-cluster(1)Cluster structuresgmx-confrms(1)Fit two structures and calculates the RMSDgmx-rms(1)Calculate RMSDs with a reference structure and RMSD matricesgmx-rmsf(1)Calculate atomic fluctuationsDistancesinstructuresovertimegmx-mindist(1)Calculate the minimum distance between two groupsgmx-mdmat(1)Calculate residue contact mapsgmx-polystat(1)Calculate static properties of polymersgmx-rmsdist(1)Calculate atom pair distances averaged with power -2, -3 or -6Massdistributionpropertiesovertimegmx-gyrate(1)Calculate the radius of gyrationgmx-msd(1)Calculates mean square displacementsgmx-polystat(1)Calculate static properties of polymersgmx-rdf(1)Calculate radial distribution functionsgmx-rotacf(1)Calculate the rotational correlation function for moleculesgmx-rotmat(1)Plot the rotation matrix for fitting to a reference structuregmx-sans(1)Compute small angle neutron scattering spectragmx-saxs(1)Compute small angle X-ray scattering spectragmx-traj(1)Plot x, v, f, box, temperature and rotational energy from trajectoriesgmx-vanhove(1)Compute Van Hove displacement and correlation functionsAnalyzingbondedinteractionsgmx-angle(1)Calculate distributions and correlations for angles and dihedralsgmx-mk_angndx(1)Generate index files for ‘gmx angle’Structuralpropertiesgmx-anadock(1)Cluster structures from Autodock runsgmx-bundle(1)Analyze bundles of axes, e.g., helicesgmx-clustsize(1)Calculate size distributions of atomic clustersgmx-disre(1)Analyze distance restraintsgmx-hbond(1)Compute and analyze hydrogen bondsgmx-order(1)Compute the order parameter per atom for carbon tailsgmx-principal(1)Calculate principal axes of inertia for a group of atomsgmx-rdf(1)Calculate radial distribution functionsgmx-saltbr(1)Compute salt bridgesgmx-sorient(1)Analyze solvent orientation around solutesgmx-spol(1)Analyze solvent dipole orientation and polarization around solutesKineticpropertiesgmx-bar(1)Calculate free energy difference estimates through Bennett’s acceptance ratiogmx-current(1)Calculate dielectric constants and current autocorrelation functiongmx-dos(1)Analyze density of states and properties based on thatgmx-dyecoupl(1)Extract dye dynamics from trajectoriesgmx-principal(1)Calculate principal axes of inertia for a group of atomsgmx-tcaf(1)Calculate viscosities of liquidsgmx-traj(1)Plot x, v, f, box, temperature and rotational energy from trajectoriesgmx-vanhove(1)Compute Van Hove displacement and correlation functionsgmx-velacc(1)Calculate velocity autocorrelation functionsElectrostaticpropertiesgmx-current(1)Calculate dielectric constants and current autocorrelation functiongmx-dielectric(1)Calculate frequency dependent dielectric constantsgmx-dipoles(1)Compute the total dipole plus fluctuationsgmx-potential(1)Calculate the electrostatic potential across the boxgmx-spol(1)Analyze solvent dipole orientation and polarization around solutesgmx-genion(1)Generate monoatomic ions on energetically favorable positionsProtein-specificanalysisgmx-do_dssp(1)Assign secondary structure and calculate solvent accessible surface areagmx-chi(1)Calculate everything you want to know about chi and other dihedralsgmx-helix(1)Calculate basic properties of alpha helicesgmx-helixorient(1)Calculate local pitch/bending/rotation/orientation inside helicesgmx-rama(1)Compute Ramachandran plotsgmx-wheel(1)Plot helical wheelsInterfacesgmx-bundle(1)Analyze bundles of axes, e.g., helicesgmx-density(1)Calculate the density of the systemgmx-densmap(1)Calculate 2D planar or axial-radial density mapsgmx-densorder(1)Calculate surface fluctuationsgmx-h2order(1)Compute the orientation of water moleculesgmx-hydorder(1)Compute tetrahedrality parameters around a given atomgmx-order(1)Compute the order parameter per atom for carbon tailsgmx-potential(1)Calculate the electrostatic potential across the boxCovarianceanalysisgmx-anaeig(1)Analyze the eigenvectorsgmx-covar(1)Calculate and diagonalize the covariance matrixgmx-make_edi(1)Generate input files for essential dynamics samplingNormalmodesgmx-anaeig(1)Analyze the normal modesgmx-nmeig(1)Diagonalize the Hessian for normal mode analysisgmx-nmtraj(1)Generate a virtual oscillating trajectory from an eigenvectorgmx-nmens(1)Generate an ensemble of structures from the normal modesgmx-grompp(1)Make a run input filegmx-mdrun(1)Find a potential energy minimum and calculate the Hessian

**COPYRIGHT**

2019, GROMACS development team