Command-line reference¶

GROMACS includes many tools for preparing, running and analyzing 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

Special topics¶

The information in these topics is also accessible through gmx help topic on the command line.

Selection syntax and usage¶

Selection syntax and usage

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 2016¶

Analysis on arbitrary subsets of atoms¶

Tools implemented in the new analysis framework can now operate upon trajectories that match only a subset of the atoms in the input structure file.

gmx insert-molecules¶

improved

gmx insert-molecules has gained an option -replace that makes it possible to insert molecules into a solvated configuration, replacing any overlapping solvent atoms. In a fully solvated box, it is also possible to insert into a certain region of the solvent only by selecting a subset of the solvent atoms (-replace takes a selection that can also contain expressions like not within 1 of ...).

gmx rdf¶

improved

The normalization for the output RDF can now also be the radial number density.

gmx genconf¶

simplified

Removed -block, -sort and -shuffle.

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.