gmx extract-cluster¶
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