Command-line reference

GROMACS includes many tools for preparing, running and analysing molecular dynamics simulations. These are all structured as part of a single gmx wrapper binary, and invoked with commands like gmx grompp. mdrun is the only other binary that can be built; in the normal build it can be run with gmx mdrun. Documentation for these can be found at the respective sections below, as well as on man pages (e.g., gmx-grompp(1)) and with gmx help command or gmx command -h.

If you’ve installed an MPI version of GROMACS, by default the gmx binary is called gmx_mpi and you should adapt accordingly.

Command-line interface and conventions

All GROMACS commands require an option before any arguments (i.e., all command-line arguments need to be preceded by an argument starting with a dash, and values not starting with a dash are arguments to the preceding option). Most options, except for boolean flags, expect an argument (or multiple in some cases) after the option name. The argument must be a separate command-line argument, i.e., separated by space, as in -f traj.xtc. If more than one argument needs to be given to an option, they should be similarly separated from each other. Some options also have default arguments, i.e., just specifying the option without any argument uses the default argument. If an option is not specified at all, a default value is used; in the case of optional files, the default might be not to use that file (see below).

All GROMACS command options start with a single dash, whether they are single- or multiple-letter options. However, two dashes are also recognized (starting from 5.1).

In addition to command-specific options, some options are handled by the gmx wrapper, and can be specified for any command. See wrapper binary help for the list of such options. These options are recognized both before the command name (e.g., gmx -quiet grompp) as well as after the command name (e.g., gmx grompp -quiet). There is also a -hidden option that can be specified in combination with -h to show help for advanced/developer-targeted options.

Most analysis commands can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.

Handling specific types of command-line options

boolean options
Boolean flags can be specified like -pbc and negated like -nopbc. It is also possible to use an explicit value like -pbc no and -pbc yes.
file name options

Options that accept files names have features that support using default file names (where the default file name is specific to that option):

  • If a required option is not set, the default is used.
  • If an option is marked optional, the file is not used unless the option is set (or other conditions make the file required).
  • If an option is set, and no file name is provided, the default is used.

All such options will accept file names without a file extension. The extension is automatically appended in such a case. When multiple input formats are accepted, such as a generic structure format, the directory will be searched for files of each type with the supplied or default name. When no file with a recognized extension is found, an error is given. For output files with multiple formats, a default file type will be used.

Some file formats can also be read from compressed (.Z or .gz) formats.

enum options
Enumerated options (enum) should be used with one of the arguments listed in the option description. The argument may be abbreviated, and the first match to the shortest argument in the list will be selected.
vector options
Some options accept a vector of values. Either 1 or 3 parameters can be supplied; when only one parameter is supplied the two other values are also set to this value.
selection options
See Selection syntax and usage.

Commands by name

  • gmx - molecular dynamics simulation suite
  • gmx anadock - Cluster structures from Autodock runs
  • gmx anaeig - Analyze eigenvectors/normal modes
  • gmx analyze - Analyze data sets
  • gmx angle - Calculate distributions and correlations for angles and dihedrals
  • gmx bar - Calculate free energy difference estimates through Bennett’s acceptance ratio
  • gmx bundle - Analyze bundles of axes, e.g., helices
  • gmx check - Check and compare files
  • gmx chi - Calculate everything you want to know about chi and other dihedrals
  • gmx cluster - Cluster structures
  • gmx clustsize - Calculate size distributions of atomic clusters
  • gmx confrms - Fit two structures and calculates the RMSD
  • gmx convert-tpr - Make a modifed run-input file
  • gmx covar - Calculate and diagonalize the covariance matrix
  • gmx current - Calculate dielectric constants and current autocorrelation function
  • gmx density - Calculate the density of the system
  • gmx densmap - Calculate 2D planar or axial-radial density maps
  • gmx densorder - Calculate surface fluctuations
  • gmx dielectric - Calculate frequency dependent dielectric constants
  • gmx dipoles - Compute the total dipole plus fluctuations
  • gmx disre - Analyze distance restraints
  • gmx distance - Calculate distances between pairs of positions
  • gmx do_dssp - Assign secondary structure and calculate solvent accessible surface area
  • gmx dos - Analyze density of states and properties based on that
  • gmx dump - Make binary files human readable
  • gmx dyecoupl - Extract dye dynamics from trajectories
  • gmx dyndom - Interpolate and extrapolate structure rotations
  • gmx editconf - Convert and manipulates structure files
  • gmx eneconv - Convert energy files
  • gmx enemat - Extract an energy matrix from an energy file
  • gmx energy - Writes energies to xvg files and display averages
  • gmx filter - Frequency filter trajectories, useful for making smooth movies
  • gmx freevolume - Calculate free volume
  • gmx gangle - Calculate angles
  • 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 grompp - Make a run input file
  • gmx gyrate - Calculate the radius of gyration
  • gmx h2order - Compute the orientation of water molecules
  • gmx hbond - Compute and analyze hydrogen bonds
  • gmx helix - Calculate basic properties of alpha helices
  • gmx helixorient - Calculate local pitch/bending/rotation/orientation inside helices
  • gmx help - Print help information
  • gmx hydorder - Compute tetrahedrality parameters around a given atom
  • gmx insert-molecules - Insert molecules into existing vacancies
  • gmx lie - Estimate free energy from linear combinations
  • gmx make_edi - Generate input files for essential dynamics sampling
  • gmx make_ndx - Make index files
  • gmx mdmat - Calculate residue contact maps
  • gmx mdrun - Perform a simulation, do a normal mode analysis or an energy minimization
  • gmx mindist - Calculate the minimum distance between two groups
  • gmx mk_angndx - Generate index files for ‘gmx angle’
  • gmx morph - Interpolate linearly between conformations
  • gmx msd - Calculates mean square displacements
  • gmx nmeig - Diagonalize the Hessian for normal mode analysis
  • gmx nmens - Generate an ensemble of structures from the normal modes
  • gmx nmtraj - Generate a virtual oscillating trajectory from an eigenvector
  • gmx order - Compute the order parameter per atom for carbon tails
  • gmx pairdist - Calculate pairwise distances between groups of positions
  • gmx pdb2gmx - Convert coordinate files to topology and FF-compliant coordinate files
  • gmx pme_error - Estimate the error of using PME with a given input file
  • gmx polystat - Calculate static properties of polymers
  • gmx potential - Calculate the electrostatic potential across the box
  • gmx principal - Calculate principal axes of inertia for a group of atoms
  • gmx rama - Compute Ramachandran plots
  • gmx rdf - Calculate radial distribution functions
  • gmx rms - Calculate RMSDs with a reference structure and RMSD matrices
  • gmx rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6
  • gmx rmsf - Calculate atomic fluctuations
  • gmx rotacf - Calculate the rotational correlation function for molecules
  • gmx rotmat - Plot the rotation matrix for fitting to a reference structure
  • gmx saltbr - Compute salt bridges
  • gmx sans - Compute small angle neutron scattering spectra
  • gmx sasa - Compute solvent accessible surface area
  • gmx saxs - Compute small angle X-ray scattering spectra
  • gmx select - Print general information about selections
  • gmx sham - Compute free energies or other histograms from histograms
  • gmx sigeps - Convert c6/12 or c6/cn combinations to and from sigma/epsilon
  • gmx solvate - Solvate a system
  • gmx sorient - Analyze solvent orientation around solutes
  • gmx spatial - Calculate the spatial distribution function
  • gmx spol - Analyze solvent dipole orientation and polarization around solutes
  • gmx tcaf - Calculate viscosities of liquids
  • gmx traj - Plot x, v, f, box, temperature and rotational energy from trajectories
  • gmx trjcat - Concatenate trajectory files
  • gmx trjconv - Convert and manipulates trajectory files
  • gmx trjorder - Order molecules according to their distance to a group
  • gmx tune_pme - Time mdrun as a function of PME ranks to optimize settings
  • gmx vanhove - Compute Van Hove displacement and correlation functions
  • gmx velacc - Calculate velocity autocorrelation functions
  • gmx view - View a trajectory on an X-Windows terminal
  • gmx wham - Perform weighted histogram analysis after umbrella sampling
  • gmx wheel - Plot helical wheels
  • gmx x2top - Generate a primitive topology from coordinates
  • gmx xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM

Commands by topic

Trajectory analysis

gmx gangle
Calculate angles
gmx distance
Calculate distances between pairs of positions
gmx freevolume
Calculate free volume
gmx pairdist
Calculate pairwise distances between groups of positions
gmx rdf
Calculate radial distribution functions
gmx sasa
Compute solvent accessible surface area
gmx select
Print general information about selections

Generating topologies and coordinates

gmx editconf
Edit the box and write subgroups
gmx x2top
Generate a primitive topology from coordinates
gmx solvate
Solvate a system
gmx insert-molecules
Insert 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 files

Running a simulation

gmx grompp
Make a run input file
gmx mdrun
Perform a simulation, do a normal mode analysis or an energy minimization
gmx convert-tpr
Make a modifed run-input file

Viewing trajectories

gmx nmtraj
Generate a virtual oscillating trajectory from an eigenvector
gmx view
View a trajectory on an X-Windows terminal

Processing energies

gmx 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 -rerun

Converting files

gmx 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 XPM

Tools

gmx 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 XPM

Distances between structures

gmx 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 fluctuations

Distances in structures over time

gmx 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 -6

Mass distribution properties over time

gmx 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 functions

Analyzing bonded interactions

gmx angle
Calculate distributions and correlations for angles and dihedrals
gmx mk_angndx
Generate index files for ‘gmx angle’

Structural properties

gmx 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 solutes

Kinetic properties

gmx 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 functions

Electrostatic properties

gmx current
Calculate dielectric constants and current autocorrelation function
gmx dielectric
Calculate 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 positions

Protein-specific analysis

gmx 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 helixorient
Calculate local pitch/bending/rotation/orientation inside helices
gmx rama
Compute Ramachandran plots
gmx wheel
Plot helical wheels

Interfaces

gmx 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 box

Covariance analysis

gmx anaeig
Analyze the eigenvectors
gmx covar
Calculate and diagonalize the covariance matrix
gmx make_edi
Generate input files for essential dynamics sampling

Normal modes

gmx 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 Hessian

Command changes between versions

Starting from GROMACS 5.0, some of the analysis commands (and a few other commands as well) have changed significantly.

One main driver for this has been that many new tools mentioned below now accept selections through one or more command-line options instead of prompting for a static index group. To take full advantage of selections, the interface to the commands has changed somewhat, and some previous command-line options are no longer present as the same effect can be achieved with suitable selections. Please see Selection syntax and usage additional information on how to use selections.

In the process, some old analysis commands have been removed in favor of more powerful functionality that is available through an alternative tool. For removed or replaced commands, this page documents how to perform the same tasks with new tools. For new commands, a brief note on the available features is given. See the linked help for the new commands for a full description.

This section lists only major changes; minor changes like additional/removed options or bug fixes are not typically included.

Version 5.1

General

Symbolic links from 5.0 are no longer supported. The only way to invoke a command is through gmx <command>.

gmx pairdist

new

gmx pairdist has been introduced as a selection-enabled replacement for gmx mindist (gmx mindist still exists unchanged). It can calculate min/max pairwise distances between a pair of selections, including, e.g., per-residue minimum distances or distances from a single point to a set of residue-centers-of-mass.

gmx rdf

rewritten

gmx rdf has been rewritten for 5.1 to use selections for specifying the points from which the RDFs are calculated. The interface is mostly the same, except that there are new command-line options to specify the selections. The following additional changes have been made:

  • -com and -rdf options have been removed. Equivalent functionality is available through selections:
    • -com can be replaced with a com of <selection> as the reference selection.
    • -rdf can be replaced with a suitable set of selections (e.g., res_com of <selection>) and/or using -seltype.
  • -rmax option is added to specify a cutoff for the RDFs. If set to a value that is significantly smaller than half the box size, it can speed up the calculation significantly if a grid-based neighborhood search can be used.
  • -hq and -fade options have been removed, as they are simply postprocessing steps on the raw numbers that can be easily done after the analysis.

Version 5.0

General

Version 5.0 introduced the gmx wrapper binary. For backwards compatibility, this version still creates symbolic links by default for old tools: e.g., g_order <options> is equivalent to gmx order <options>, and g_order is simply a symbolic link on the file system.

g_bond

replaced

This tool has been removed in 5.0. A replacement is gmx distance.

You can provide your existing index file to gmx distance, and it will calculate the same distances. The differences are:

  • -blen and -tol options have different default values.
  • You can control the output histogram with -binw.
  • -aver and -averdist options are not present. Instead, you can choose between the different things to calculate using -oav (corresponds to -d with -averdist), -oall (corresponds to -d without -averdist), -oh (corresponds to -o with -aver), and -oallstat (corresponds to -l without -aver).

You can produce any combination of output files. Compared to g_bond, gmx distance -oall is currently missing labels for the output columns.

g_dist

replaced

This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).

If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:

gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall

The -intra switch is replaced with -nopbc.

If you used -dist D, you can do the same calculation with gmx select:

gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt

You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt)

gmx distance

new

gmx distance has been introduced as a selection-enabled replacement for various tools that computed distances between fixed pairs of atoms (or centers-of-mass of groups). It has a combination of the features of g_bond and g_dist, allowing computation of one or multiple distances, either between atom-atom pairs or centers-of-mass of groups, and providing a combination of output options that were available in one of the tools.

gmx gangle

new

gmx gangle has been introduced as a selection-enabled replacement for g_sgangle. In addition to supporting atom-atom vectors, centers-of-mass can be used as endpoints of the vectors, and there are a few additional angle types that can be calculated. The command also has basic support for calculating normal angles between three atoms and/or centers-of-mass, making it a partial replacement for gmx angle as well.

gmx protonate

replaced

This was a very old tool originally written for united atom force fields, where it was necessary to generate all hydrogens after running a trajectory in order to calculate e.g. distance restraint violations. The functionality to simply protonate a structure is available in gmx pdb2gmx. If there is significant interest, we might reintroduce it after moving to new topology formats in the future.

gmx freevolume

new

This tool has been introduced in 5.0. It uses a Monte Carlo sampling method to calculate the fraction of free volume within the box (using a probe of a given size).

g_sas

rewritten

This tool has been rewritten in 5.0, and renamed to gmx sasa (the underlying surface area calculation algorithm is still the same).

The main difference in the new tool is support for selections. Instead of prompting for an index group, a (potentially dynamic) selection for the calculation can be given with -surface. Any number of output groups can be given with -output, allowing multiple parts of the surface area to be computed in a single run. The total area of the -surface group is now always calculated.

The tool no longer automatically divides the surface into hydrophobic and hydrophilic areas, and there is no -f_index option. The same effects can be obtained by defining suitable selections for -output. If you want output that contains the same numbers as with the old tool for a calculation group A and output group B, you can use

gmx sasa -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"'

Solvation free energy estimates are now calculated only if separately requested with -odg, and are written into a separate file.

Output option -i for a position restraint file is not currently implemented in the new tool, but would not be very difficult to add if requested.

g_sgangle

replaced

This tool has been removed in 5.0. A replacement is gmx gangle (for angle calculation) and gmx distance (for -od, -od1, -od2).

If you had index groups A and B in index.ndx for g_sgangle, you can use the following command to compute the same angle with gmx gangle:

gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 vector/plane -group2 'group "B"' -oav

You need to select either vector or plane for the -g1 and -g2 options depending on which one your index groups specify.

If you only had a single index group A in index.ndx and you used g_sgangle -z or -one, you can use:

gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 z/t0 -oav

For the distances, you can use gmx distance to compute one or more distances as you want. Both distances between centers of groups or individual atoms are supported using the new selection syntax.

genbox

This tool has been split to gmx solvate and gmx insert-molecules.

tpbconv

This tool has been renamed gmx convert-tpr.