GMX(1)

💖 GMX(1) — the GROMACS girlie manual 💖

okay so. hi bestie. this is gmx, the main character of the GROMACS molecular dynamics simulation suite. she's on the GROMACS man page, section 1, and she is that girl.

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✨ NAME ✨

gmx — molecular dynamics simulation suite 🧚

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🌈 SYNOPSIS 🌈

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

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💅 DESCRIPTION 💅

GROMACS is a full-featured suite of programs for running molecular dynamics simulations, aka simulating how systems of hundreds to millions of particles behave using Newtonian equations of motion. no cap, that's literally the whole vibe.

it's mainly used for research on proteins, lipids, and polymers, but honestly it can be applied to a huge variety of chemical and biological research questions. versatile queen. 👑

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🌸 OPTIONS 🌸

Other options, bestie:

• -[no]h (no) — prints help and then dips out immediately
• -[no]quiet (no) — stops her from printing the usual startup info or quotes
• -[no]version (no) — prints the extended version info and quits
• -[no]copyright (no) — prints the copyright info on startup
• -nice <int> (19) — sets the nicelevel (the default actually depends on the command, fyi)
• -[no]backup (yes) — writes backups whenever output files already exist

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👑 GMX COMMANDS 👑

here's the whole lineup of commands you can run. for the deets on any one of them, go read their own man pages, or hit gmx help <command>. 🫶

🦋 Trajectory analysis 🦋

• gmx-gangle(1) — calculates angles
• gmx-convert-trj(1) — converts between different trajectory types
• gmx-distance(1) — calculates the distances between pairs of positions
• gmx-dssp(1) — calculates protein secondary structure using the DSSP algorithm
• gmx-extract-cluster(1) — lets you pull out the frames that correspond to specific clusters from a trajectory
• gmx-freevolume(1) — calculates free volume
• gmx-hbond(1) — computes and analyzes hydrogen bonds
• gmx-msd(1) — computes mean squared displacements
• gmx-pairdist(1) — calculates pairwise distances between groups of positions
• gmx-rdf(1) — calculates radial distribution functions
• gmx-sasa(1) — computes solvent accessible surface area
• gmx-scattering(1) — calculates small angle scattering profiles for SANS or SAXS
• gmx-select(1) — prints general info about selections
• gmx-trajectory(1) — prints coordinates, velocities, and/or forces for selections
• gmx-gyrate(1) — calculates the radius of gyration of a molecule

🌸 Generating topologies and coordinates 🌸

• gmx-editconf(1) — edits the box and writes subgroups
• gmx-x2top(1) — generates a primitive topology from coordinates
• gmx-solvate(1) — solvates a system
• gmx-insert-molecules(1) — inserts molecules into existing vacancies
• gmx-genconf(1) — multiplies a conformation in 'random' orientations
• gmx-genion(1) — generates monoatomic ions on energetically favorable positions
• gmx-genrestr(1) — generates position restraints or distance restraints for index groups
• gmx-pdb2gmx(1) — converts coordinate files into topology and FF-compliant coordinate files

🔥 Running a simulation 🔥

• gmx-grompp(1) — makes a run input file
• gmx-mdrun(1) — performs a simulation, does a normal mode analysis, or does an energy minimization
• gmx-convert-tpr(1) — makes a modified run-input file

🎀 Viewing trajectories 🎀

• gmx-nmtraj(1) — generates a virtual oscillating trajectory from an eigenvector

💜 Processing energies 💜

• gmx-enemat(1) — extracts an energy matrix from an energy file
• gmx-energy(1) — writes energies to xvg files and displays averages
• gmx-mdrun(1) — (re)calculates energies for trajectory frames with -rerun

⭐ Converting files ⭐

• gmx-editconf(1) — converts and manipulates structure files
• gmx-eneconv(1) — converts energy files
• gmx-sigeps(1) — converts c6/12 or c6/cn combinations to and from sigma/epsilon
• gmx-trjcat(1) — concatenates trajectory files
• gmx-trjconv(1) — converts and manipulates trajectory files
• gmx-xpm2ps(1) — converts XPM (XPixelMap) matrices to postscript or XPM

🧚 Tools 🧚

• gmx-analyze(1) — analyzes data sets
• gmx-awh(1) — extracts data from an accelerated weight histogram (AWH) run
• gmx-filter(1) — frequency filters trajectories, which is lowkey useful for making smooth movies
• gmx-lie(1) — estimates free energy from linear combinations
• gmx-pme_error(1) — estimates the error of using PME with a given input file
• gmx-sham(1) — computes free energies or other histograms from histograms
• gmx-spatial(1) — calculates the spatial distribution function
• gmx-traj(1) — plots x, v, f, box, temperature and rotational energy from trajectories
• gmx-tune_pme(1) — times mdrun as a function of PME ranks so you can optimize your settings
• gmx-wham(1) — performs weighted histogram analysis after umbrella sampling
• gmx-check(1) — checks and compares files
• gmx-dump(1) — makes binary files human readable
• gmx-make_ndx(1) — makes index files
• gmx-mk_angndx(1) — generates index files for 'gmx angle'
• gmx-trjorder(1) — orders molecules according to their distance to a group
• gmx-xpm2ps(1) — converts XPM (XPixelMap) matrices to postscript or XPM
• gmx-report-methods(1) — writes a short summary about the simulation setup to a text file and/or to the standard output

🍓 Distances between structures 🍓

• gmx-cluster(1) — clusters structures
• gmx-confrms(1) — fits two structures and calculates the RMSD
• gmx-rms(1) — calculates RMSDs with a reference structure and RMSD matrices
• gmx-rmsf(1) — calculates atomic fluctuations

🌈 Distances in structures over time 🌈

• gmx-mindist(1) — calculates the minimum distance between two groups
• gmx-mdmat(1) — calculates residue contact maps
• gmx-polystat(1) — calculates static properties of polymers
• gmx-rmsdist(1) — calculates atom pair distances averaged with power -2, -3 or -6

🎀 Mass distribution properties over time 🎀

• gmx-gyrate-legacy(1) — calculates the radius of gyration
• gmx-polystat(1) — calculates static properties of polymers
• gmx-rdf(1) — calculates radial distribution functions
• gmx-rotacf(1) — calculates the rotational correlation function for molecules
• gmx-rotmat(1) — plots the rotation matrix for fitting to a reference structure
• gmx-sans-legacy(1) — computes small angle neutron scattering spectra
• gmx-saxs-legacy(1) — computes small angle X-ray scattering spectra
• gmx-traj(1) — plots x, v, f, box, temperature and rotational energy from trajectories
• gmx-vanhove(1) — computes Van Hove displacement and correlation functions

💖 Analyzing bonded interactions 💖

• gmx-angle(1) — calculates distributions and correlations for angles and dihedrals
• gmx-mk_angndx(1) — generates index files for 'gmx angle'

💜 Structural properties 💜

• gmx-bundle(1) — analyzes bundles of axes, e.g., helices
• gmx-clustsize(1) — calculates size distributions of atomic clusters
• gmx-disre(1) — analyzes distance restraints
• gmx-hbond-legacy(1) — computes and analyzes hydrogen bonds
• gmx-order(1) — computes the order parameter per atom for carbon tails
• gmx-principal(1) — calculates principal axes of inertia for a group of atoms
• gmx-rdf(1) — calculates radial distribution functions
• gmx-saltbr(1) — computes salt bridges
• gmx-sorient(1) — analyzes solvent orientation around solutes
• gmx-spol(1) — analyzes solvent dipole orientation and polarization around solutes

🔥 Kinetic properties 🔥

• gmx-bar(1) — calculates free energy difference estimates through Bennett's acceptance ratio
• gmx-current(1) — calculates dielectric constants and the current autocorrelation function
• gmx-dos(1) — analyzes density of states and properties based on that
• gmx-dyecoupl(1) — extracts dye dynamics from trajectories
• gmx-principal(1) — calculates principal axes of inertia for a group of atoms
• gmx-tcaf(1) — calculates viscosities of liquids
• gmx-traj(1) — plots x, v, f, box, temperature and rotational energy from trajectories
• gmx-vanhove(1) — computes Van Hove displacement and correlation functions
• gmx-velacc(1) — calculates velocity autocorrelation functions

⚡ Electrostatic properties ⚡

• gmx-current(1) — calculates dielectric constants and the current autocorrelation function
• gmx-dielectric(1) — calculates frequency dependent dielectric constants
• gmx-dipoles(1) — computes the total dipole plus fluctuations
• gmx-potential(1) — calculates the electrostatic potential across the box
• gmx-spol(1) — analyzes solvent dipole orientation and polarization around solutes
• gmx-genion(1) — generates monoatomic ions on energetically favorable positions

🧬 Protein-specific analysis 🧬

• gmx-chi(1) — calculates everything you want to know about chi and other dihedrals
• gmx-helix(1) — calculates basic properties of alpha helices
• gmx-helixorient(1) — calculates local pitch/bending/rotation/orientation inside helices
• gmx-rama(1) — computes Ramachandran plots
• gmx-wheel(1) — plots helical wheels

🦋 Interfaces 🦋

• gmx-bundle(1) — analyzes bundles of axes, e.g., helices
• gmx-density(1) — calculates the density of the system
• gmx-densmap(1) — calculates 2D planar or axial-radial density maps
• gmx-densorder(1) — calculates surface fluctuations
• gmx-h2order(1) — computes the orientation of water molecules
• gmx-hydorder(1) — computes tetrahedrality parameters around a given atom
• gmx-order(1) — computes the order parameter per atom for carbon tails
• gmx-potential(1) — calculates the electrostatic potential across the box

✨ Covariance analysis ✨

• gmx-anaeig(1) — analyzes the eigenvectors
• gmx-covar(1) — calculates and diagonalizes the covariance matrix
• gmx-make_edi(1) — generates input files for essential dynamics sampling

🌟 Normal modes 🌟

• gmx-anaeig(1) — analyzes the normal modes
• gmx-nmeig(1) — diagonalizes the Hessian for normal mode analysis
• gmx-nmtraj(1) — generates a virtual oscillating trajectory from an eigenvector
• gmx-nmens(1) — generates an ensemble of structures from the normal modes
• gmx-grompp(1) — makes a run input file
• gmx-mdrun(1) — finds a potential energy minimum and calculates the Hessian

💖 COPYRIGHT 💖

okay so the legal bit, and it's short and sweet bestie, don't stress 🫶

This whole page — every flag, every command, every little ✨ vibe ✨ — belongs to the GROMACS development team, copyright 2026. That's it. That's the whole copyright notice. They made it, they own it, we just read the manual and say thank you 💅👑

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and that's a wrap on GMX(1), bestie!! 🎀 you made it all the way to the end, which is honestly iconic behaviour, lowkey main character energy fr fr 💜🦋

this page is from GROMACS 2026.4, dated Oct 02, 2026 ⭐

go run some simulations, hydrate, and remember: read the error message before you panic 😭🌸 bye pookie!! ✨👑