GMX(1) | GROMACS | GMX(1) |

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

**-[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-gangle(1)**- Calculate angles

**gmx-distance(1)**- Calculate distances between pairs of positions

**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-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 'random' 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

**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

**gmx-nmtraj(1)**- Generate a virtual oscillating trajectory from an eigenvector

**gmx-view(1)**- View a trajectory on an X-Windows terminal

**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

**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

**gmx-analyze(1)**- Analyze data sets

**gmx-dyndom(1)**- Interpolate and extrapolate structure rotations

**gmx-filter(1)**- Frequency filter trajectories, useful for making smooth movies

**gmx-lie(1)**- Estimate free energy from linear combinations

**gmx-morph(1)**- Interpolate linearly between conformations

**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 trajectories

**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 'gmx angle'

**gmx-trjorder(1)**- Order molecules according to their distance to a group

**gmx-xpm2ps(1)**- Convert XPM (XPixelMap) matrices to postscript or XPM

**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

**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

**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 trajectories

**gmx-vanhove(1)**- Compute Van Hove displacement and correlation functions

**gmx-angle(1)**- Calculate distributions and correlations for angles and dihedrals

**gmx-mk_angndx(1)**- Generate index files for 'gmx angle'

**gmx-anadock(1)**- Cluster structures from Autodock runs

**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

**gmx-bar(1)**- Calculate free energy difference estimates through Bennett's acceptance ratio

**gmx-current(1)**- Calculate dielectric constants and current autocorrelation function

**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 trajectories

**gmx-vanhove(1)**- Compute Van Hove displacement and correlation functions

**gmx-velacc(1)**- Calculate velocity autocorrelation functions

**gmx-current(1)**- Calculate dielectric constants and current autocorrelation function

**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

**gmx-do_dssp(1)**- Assign secondary structure and calculate solvent accessible surface area

**gmx-chi(1)**- Calculate everything you want to know about chi and other dihedrals

**gmx-helix(1)**- Calculate basic properties of alpha helices

**gmx-helixorient(1)**- Calculate local pitch/bending/rotation/orientation inside helices

**gmx-rama(1)**- Compute Ramachandran plots

**gmx-wheel(1)**- Plot helical wheels

**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

**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

**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

September 15, 2017 | 2016.4 |