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:
-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
-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, obtained 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 cluster.: xtc trr cpt gro g96 pdb tng
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: none, xmgrace, xmgr
-[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
SEE ALSO
More information about GROMACS is available at <- http://www.gromacs.org/>.
COPYRIGHT
2020, GROMACS development team