GMX-EXTRACT-CLUSTER(1)

✨ NAME ✨

gmx-extract-cluster — the girlies' way to pull out frames that match clusters from a trajectory 💅

So this is GMX-EXTRACT-CLUSTER(1) from the GROMACS manual, and bestie, it's literally the tool that goes and grabs you exactly the frames you asked for. Let's go 🦋

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🌸 SYNOPSIS 🌸

gmx extract-cluster [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
            [-n [<.ndx>]] [-clusters [<.ndx>]]
            [-o [<.xtc/.trr/...>]] [-b <time>] [-e <time>]
            [-dt <time>] [-tu <enum>] [-fgroup <selection>]
            [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
            [-selrpos <enum>] [-select <selection>] [-vel <enum>]
            [-force <enum>] [-atoms <enum>] [-precision <int>]
            [-starttime <time>] [-timestep <time>] [-box <vector>]

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💖 DESCRIPTION 💖

Okay so picture this: gmx extract-cluster is the module you run to pull out the trajectory frames that correspond to clusters. And where do those clusters come from? From running gmx cluster with the -clndx option, periodt. 🎀

And the range?? The module supports writing all GROMACS supported trajectory file formats. All of them. She ate. 🔥

Also included: a whole selection of possible options to change additional information. Little extras, whatever you need. ✨

And big news — it is possible to write only a selection of atoms to the output trajectory files, for each cluster. So you're not obligated to take the whole squad along. 🌈

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👑 OPTIONS 👑

🧚 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — Input trajectory or single configuration. Formats she eats: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — Input structure. Formats: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) (Optional) — Extra index groups, in case you need a lil something extra 💜
• -clusters [<.ndx>] (cluster.ndx) — Name of index file containing frame indices for each cluster, obtained from gmx cluster -clndx. This one is the whole point bestie, no cap 🔑

🎀 Options to specify output files:

• -o [<.xtc/.trr/...>] (trajout.xtc) — Prefix for the name of the trajectory file written for each cluster.: xtc trr cpt gro g96 pdb tng h5md

💫 Other options:

• -b <time> (0) — First frame (ps) to read from trajectory
• -e <time> (0) — Last frame (ps) to read from trajectory
• -dt <time> (0) — Only use frame if t MOD dt == first time (ps)
• -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s
• -fgroup <selection> — Atoms stored in the trajectory file (if not set, assume first N atoms)
• -xvg <enum> (xmgrace) — Plot formatting: xmgrace, xmgr, none
• -[no]rmpbc (yes) — Make molecules whole for each frame
• -[no]pbc (yes) — Use periodic boundary conditions for distance calculation
• -sf <file> — Provide selections from files
• -selrpos <enum> (atom) — Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
• -select <selection> — Selection of atoms to write to the file
• -vel <enum> (preserved-if-present) — Save velocities from frame if possible: preserved-if-present, always, never
• -force <enum> (preserved-if-present) — Save forces from frame if possible: preserved-if-present, always, never
• -atoms <enum> (preserved-if-present) — Decide on providing new atom information from topology or using current frame atom information: preserved-if-present, always-from-structure, never, always
• -precision <int> (3) — Set output precision to custom value
• -starttime <time> (0) — Change start time for first frame
• -timestep <time> (0) — Change time between different frames
• -box <vector> — New diagonal box vector for output frame

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🫶 SEE ALSO 🫶

• gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

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💀 COPYRIGHT 💀

2026, GROMACS development team

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okay that's the whole page, you're so welcome 💅 go extract some clusters, main character energy only ✨

Version 2026.4 🌸 — dated Oct 02, 2026 🎀 — and that's the vibe check, bestie, ily, bye 🦋💖