Man page - gmx-extract-cluster(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
- gmx-genrestr(1)
- gmx-bar(1)
- gmx-lie(1)
- gmx-filter(1)
- gmx-scattering(1)
- gmx-anaeig(1)
- gmx-covar(1)
- gmx_d(1)
- gmx-genconf(1)
- gmx-mdrun(1)
- gmx-velacc(1)
- gmx-tcaf(1)
- gmx-insert-molecules(1)
- gmx-bundle(1)
- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
- gmx-confrms(1)
- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
- gmx-current(1)
- gmx-freevolume(1)
- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
- gmx-gyrate(1)
- gmx-solvate(1)
- gmx-densmap(1)
- gmx-rotacf(1)
- gmx-helix(1)
- gmx_mpi(1)
- gmx-convert-tpr(1)
- gmx-convert-trj(1)
- gmx-polystat(1)
- gmx-angle(1)
- gmx-xpm2ps(1)
- gmx-pdb2gmx(1)
- gmx-sasa(1)
- gmx-x2top(1)
- gmx-trjcat(1)
- gmx-h2order(1)
- gmx-nmr(1)
- gmx-dump(1)
- gmx-spol(1)
- gmx-distance(1)
- gmx-clustsize(1)
- gmx-rama(1)
- gmx-chi(1)
- gmx-pme_error(1)
- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
- gmx-tune_pme(1)
- gmx-grompp(1)
- gmx-make_edi(1)
- gmx-trajectory(1)
- gmx-dipoles(1)
- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
- gmx-analyze(1)
- demux(1)
- gmx-disre(1)
- gmx-saxs-legacy(1)
- gmx-sigeps(1)
- gmx-mdmat(1)
- xplor2gmx(1)
- gmx-check(1)
- gmx-vanhove(1)
- gmx-dssp(1)
- gmx-densorder(1)
- gmx-principal(1)
- gmx-mindist(1)
- gmx-spatial(1)
- gmx-wham(1)
- gmx-rmsf(1)
- gmx-dos(1)
- gmx-mk_angndx(1)
- gmx-nmens(1)
- gmx-dielectric(1)
- gmx-sorient(1)
- gmx-help(1)
- gmx-hbond-legacy(1)
- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-EXTRACT-CLUSTER
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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: 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, 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
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team