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-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 trajectory
- 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 ‘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-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 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-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 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-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