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

       2024, GROMACS development team