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**PROGRAM:**

**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 or

**gmx**

**help**

**<command>**for further details.

**Trajectory**

**analysis**

__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

**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 '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

**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-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

**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 trajectories

__gmx-vanhove(1)__

Compute Van Hove displacement and correlation functions

**Analyzing**

**bonded**

**interactions**

__gmx-angle(1)__

Calculate distributions and correlations for angles and dihedrals

__gmx-mk_angndx(1)__

Generate index files for 'gmx angle'

**Structural**

**properties**

__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

**Kinetic**

**properties**

__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

**Electrostatic**

**properties**

__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

**Protein-specific**

**analysis**

__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

**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**

2015, GROMACS development team

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