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gmx-extract-cluster - Allows extracting frames corresponding to clusters from trajectory


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>]


gmx extract-cluster can be used to extract trajectory frames that correspond 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 information.

It is possible to write only a selection of atoms to the output trajectory files for each cluster.


Options to specify input files:

Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
Input structure: tpr gro g96 pdb brk ent
Extra index groups
Name of index file containing frame indices for each cluster, obtained from gmx cluster -clndx.

Options to specify output files:

Prefix for the name of the trajectory file written for each cluster.: xtc trr cpt gro g96 pdb tng

Other options:

First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
Provide selections from files
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
Selection of atoms to write to the file
Save velocities from frame if possible: preserved-if-present, always, never
Save forces from frame if possible: preserved-if-present, always, never
Decide on providing new atom information from topology or using current frame atom information: preserved-if-present, always-from-structure, never, always
Set output precision to custom value
Change start time for first frame
Change time between different frames
New diagonal box vector for output frame



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2022, GROMACS development team

June 16, 2022 2022.2