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GMX(1) GROMACS GMX(1) 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 dy- namics simulations, i.e., to simulate the behavior of systems with hun- dreds 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 or gmx help <command> for further details. Trajectory analysis gmx-gangle(1) Calculate angles gmx-convert-trj(1) Converts between different trajectory types gmx-distance(1) Calculate distances between pairs of positions gmx-extract-cluster(1) Allows extracting frames corresponding to clusters from trajec- tory gmx-freevolume(1) Calculate free volume gmx-pairdist(1) Calculate pairwise distances between groups of positions gmx-rdf(1) Calculate radial distribution functions gmx-sasa(1) Compute solvent accessible surface area gmx-select(1) Print general information about selections gmx-trajectory(1) Print coordinates, velocities, and/or forces for selections Generating topologies and coordinates gmx-editconf(1) Edit the box and write subgroups gmx-x2top(1) Generate a primitive topology from coordinates gmx-solvate(1) Solvate a system gmx-insert-molecules(1) Insert molecules into existing vacancies gmx-genconf(1) Multiply a conformation in arandoma orientations gmx-genion(1) Generate monoatomic ions on energetically favorable positions gmx-genrestr(1) Generate position restraints or distance restraints for index groups gmx-pdb2gmx(1) Convert coordinate files to topology and FF-compliant coordinate files Running a simulation gmx-grompp(1) Make a run input file gmx-mdrun(1) Perform a simulation, do a normal mode analysis or an energy minimization gmx-convert-tpr(1) Make a modifed run-input file Viewing trajectories gmx-nmtraj(1) Generate a virtual oscillating trajectory from an eigenvector gmx-view(1) View a trajectory on an X-Windows terminal Processing energies gmx-enemat(1) Extract an energy matrix from an energy file gmx-energy(1) Writes energies to xvg files and display averages gmx-mdrun(1) (Re)calculate energies for trajectory frames with -rerun Converting files gmx-editconf(1) Convert and manipulates structure files gmx-eneconv(1) Convert energy files gmx-sigeps(1) Convert c6/12 or c6/cn combinations to and from sigma/epsilon gmx-trjcat(1) Concatenate trajectory files gmx-trjconv(1) Convert and manipulates trajectory files gmx-xpm2ps(1) Convert XPM (XPixelMap) matrices to postscript or XPM Tools gmx-analyze(1) Analyze data sets gmx-awh(1) Extract data from an accelerated weight histogram (AWH) run gmx-filter(1) Frequency filter trajectories, useful for making smooth movies gmx-lie(1) Estimate free energy from linear combinations gmx-pme_error(1) Estimate the error of using PME with a given input file gmx-sham(1) Compute free energies or other histograms from histograms gmx-spatial(1) Calculate the spatial distribution function gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from tra- jectories gmx-tune_pme(1) Time mdrun as a function of PME ranks to optimize settings gmx-wham(1) Perform weighted histogram analysis after umbrella sampling gmx-check(1) Check and compare files gmx-dump(1) Make binary files human readable gmx-make_ndx(1) Make index files gmx-mk_angndx(1) Generate index files for agmx anglea gmx-trjorder(1) Order molecules according to their distance to a group gmx-xpm2ps(1) Convert XPM (XPixelMap) matrices to postscript or XPM gmx-report-methods(1) Write short summary about the simulation setup to a text file and/or to the standard output. Distances between structures gmx-cluster(1) Cluster structures gmx-confrms(1) Fit two structures and calculates the RMSD gmx-rms(1) Calculate RMSDs with a reference structure and RMSD matrices gmx-rmsf(1) Calculate atomic fluctuations Distances in structures over time gmx-mindist(1) Calculate the minimum distance between two groups gmx-mdmat(1) Calculate residue contact maps gmx-polystat(1) Calculate static properties of polymers gmx-rmsdist(1) Calculate atom pair distances averaged with power -2, -3 or -6 Mass distribution properties over time gmx-gyrate(1) Calculate the radius of gyration gmx-msd(1) Calculates mean square displacements gmx-polystat(1) Calculate static properties of polymers gmx-rdf(1) Calculate radial distribution functions gmx-rotacf(1) Calculate the rotational correlation function for molecules gmx-rotmat(1) Plot the rotation matrix for fitting to a reference structure gmx-sans(1) Compute small angle neutron scattering spectra gmx-saxs(1) Compute small angle X-ray scattering spectra gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from tra- jectories gmx-vanhove(1) Compute Van Hove displacement and correlation functions Analyzing bonded interactions gmx-angle(1) Calculate distributions and correlations for angles and dihe- drals gmx-mk_angndx(1) Generate index files for agmx anglea Structural properties gmx-bundle(1) Analyze bundles of axes, e.g., helices gmx-clustsize(1) Calculate size distributions of atomic clusters gmx-disre(1) Analyze distance restraints gmx-hbond(1) Compute and analyze hydrogen bonds gmx-order(1) Compute the order parameter per atom for carbon tails gmx-principal(1) Calculate principal axes of inertia for a group of atoms gmx-rdf(1) Calculate radial distribution functions gmx-saltbr(1) Compute salt bridges gmx-sorient(1) Analyze solvent orientation around solutes gmx-spol(1) Analyze solvent dipole orientation and polarization around solutes Kinetic properties gmx-bar(1) Calculate free energy difference estimates through Bennettas ac- ceptance ratio gmx-current(1) Calculate dielectric constants and current autocorrelation func- tion gmx-dos(1) Analyze density of states and properties based on that gmx-dyecoupl(1) Extract dye dynamics from trajectories gmx-principal(1) Calculate principal axes of inertia for a group of atoms gmx-tcaf(1) Calculate viscosities of liquids gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from tra- jectories gmx-vanhove(1) Compute Van Hove displacement and correlation functions gmx-velacc(1) Calculate velocity autocorrelation functions Electrostatic properties gmx-current(1) Calculate dielectric constants and current autocorrelation func- tion gmx-dielectric(1) Calculate frequency dependent dielectric constants gmx-dipoles(1) Compute the total dipole plus fluctuations gmx-potential(1) Calculate the electrostatic potential across the box gmx-spol(1) Analyze solvent dipole orientation and polarization around solutes gmx-genion(1) Generate monoatomic ions on energetically favorable positions Protein-specific analysis gmx-do_dssp(1) Assign secondary structure and calculate solvent accessible sur- face area gmx-chi(1) Calculate everything you want to know about chi and other dihe- drals gmx-helix(1) Calculate basic properties of alpha helices gmx-helixorient(1) Calculate local pitch/bending/rotation/orientation inside he- lices gmx-rama(1) Compute Ramachandran plots gmx-wheel(1) Plot helical wheels Interfaces gmx-bundle(1) Analyze bundles of axes, e.g., helices gmx-density(1) Calculate the density of the system gmx-densmap(1) Calculate 2D planar or axial-radial density maps gmx-densorder(1) Calculate surface fluctuations gmx-h2order(1) Compute the orientation of water molecules gmx-hydorder(1) Compute tetrahedrality parameters around a given atom gmx-order(1) Compute the order parameter per atom for carbon tails gmx-potential(1) Calculate the electrostatic potential across the box Covariance analysis gmx-anaeig(1) Analyze the eigenvectors gmx-covar(1) Calculate and diagonalize the covariance matrix gmx-make_edi(1) Generate input files for essential dynamics sampling Normal modes gmx-anaeig(1) Analyze the normal modes gmx-nmeig(1) Diagonalize the Hessian for normal mode analysis gmx-nmtraj(1) Generate a virtual oscillating trajectory from an eigenvector gmx-nmens(1) Generate an ensemble of structures from the normal modes gmx-grompp(1) Make a run input file gmx-mdrun(1) Find a potential energy minimum and calculate the Hessian COPYRIGHT 2020, GROMACS development team 2020.4 Oct 06, 2020 GMX(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | GMX COMMANDS | COPYRIGHT
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