gmx-extract-cluster - Allows extracting frames corresponding to clusters from trajectory

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                            GMX-EXTRACT-CLUSTER(1)

gmxextract-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.

       gmx-extract-cluster - Allows extracting frames corresponding to clusters from trajectory

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)(Optional)
              Input trajectory or single configuration: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Input structure: tprgrog96pdb 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.: xtctrrcptgrog96pdbtng

       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

gmx(1)

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

          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>]