GMX-EXTRACT-CLUSTER(1) GROMACS GMX-EXTRACT-CLUSTER(1) NAME gmx-extract-cluster - Allows extracting frames corresponding to clusters from trajectory 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>] DESCRIPTION gmx extract-cluster can be used to extract trajectory frames that corre- spond to clusters obtained from running gmx cluster with the -clndx option. The module supports writing all GROMACS supported trajectory file formats. Included is also a selection of possible options to change additional in- formation. It is possible to write only a selection of atoms to the output trajectory files for each cluster. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) (Optional) Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md -s [<.tpr/.gro/...>] (topol.tpr) (Optional) Input structure: tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Extra index groups -clusters [<.ndx>] (cluster.ndx) Name of index file containing frame indices for each cluster, ob- tained from gmx cluster -clndx. Options to specify output files: -o [<.xtc/.trr/...>] (trajout.xtc) Prefix for the name of the trajectory file written for each clus- ter.: 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, al- ways, 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 cur- rent frame atom information: preserved-if-present, al- ways-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 SEE ALSO gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>. COPYRIGHT 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-EXTRACT-CLUSTER(1)
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