Scroll to navigation

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 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

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: none, xmgrace, xmgr
-[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

SEE ALSO

gmx(1)

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

COPYRIGHT

2021, GROMACS development team

March 29, 2021 2020.6-Debian-2020.6-2