1GMX-EXTRACT-CLUSTER(1)              GROMACS             GMX-EXTRACT-CLUSTER(1)
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NAME

6       gmx-extract-cluster  -  Allows extracting frames corresponding to clus‐
7       ters from trajectory
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SYNOPSIS

10          gmx extract-cluster [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
11                       [-n [<.ndx>]] [-clusters [<.ndx>]]
12                       [-o [<.xtc/.trr/...>]] [-b <time>] [-e <time>]
13                       [-dt <time>] [-tu <enum>] [-fgroup <selection>]
14                       [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
15                       [-selrpos <enum>] [-select <selection>] [-vel <enum>]
16                       [-force <enum>] [-atoms <enum>] [-precision <int>]
17                       [-starttime <time>] [-timestep <time>] [-box <vector>]
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DESCRIPTION

20       gmx extract-cluster can be used to extract trajectory frames that  cor‐
21       respond  to  clusters obtained from running gmx cluster with the -clndx
22       option.  The module supports writing all GROMACS  supported  trajectory
23       file formats.
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25       Included  is  also a selection of possible options to change additional
26       information.
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28       It is possible to write only a selection of atoms to the output trajec‐
29       tory files for each cluster.
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OPTIONS

32       Options to specify input files:
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34       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
35              Input  trajectory  or  single configuration: xtc trr cpt gro g96
36              pdb tng
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38       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
39              Input structure: tpr gro g96 pdb brk ent
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41       -n [<.ndx>] (index.ndx) (Optional)
42              Extra index groups
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44       -clusters [<.ndx>] (cluster.ndx)
45              Name of index file containing frame indices  for  each  cluster,
46              obtained from gmx cluster -clndx.
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48       Options to specify output files:
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50       -o [<.xtc/.trr/...>] (trajout.xtc)
51              Prefix  for  the  name  of  the trajectory file written for each
52              cluster.: xtc trr cpt gro g96 pdb tng
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54       Other options:
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56       -b <time> (0)
57              First frame (ps) to read from trajectory
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59       -e <time> (0)
60              Last frame (ps) to read from trajectory
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62       -dt <time> (0)
63              Only use frame if t MOD dt == first time (ps)
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65       -tu <enum> (ps)
66              Unit for time values: fs, ps, ns, us, ms, s
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68       -fgroup <selection>
69              Atoms stored in the trajectory file (if not set, assume first  N
70              atoms)
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72       -xvg <enum> (xmgrace)
73              Plot formatting: xmgrace, xmgr, none
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75       -[no]rmpbc (yes)
76              Make molecules whole for each frame
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78       -[no]pbc (yes)
79              Use periodic boundary conditions for distance calculation
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81       -sf <file>
82              Provide selections from files
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84       -selrpos <enum> (atom)
85              Selection  reference positions: atom, res_com, res_cog, mol_com,
86              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
87              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
88              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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90       -select <selection>
91              Selection of atoms to write to the file
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93       -vel <enum> (preserved-if-present)
94              Save velocities from frame  if  possible:  preserved-if-present,
95              always, never
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97       -force <enum> (preserved-if-present)
98              Save  forces  from  frame if possible: preserved-if-present, al‐
99              ways, never
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101       -atoms <enum> (preserved-if-present)
102              Decide on providing new atom information from topology or  using
103              current   frame   atom  information:  preserved-if-present,  al‐
104              ways-from-structure, never, always
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106       -precision <int> (3)
107              Set output precision to custom value
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109       -starttime <time> (0)
110              Change start time for first frame
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112       -timestep <time> (0)
113              Change time between different frames
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115       -box <vector>
116              New diagonal box vector for output frame
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SEE ALSO

119       gmx(1)
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121       More    information    about    GROMACS    is    available    at     <‐
122       http://www.gromacs.org/>.
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125       2022, GROMACS development team
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1302022.3                           Sep 02, 2022           GMX-EXTRACT-CLUSTER(1)
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