1GMX-CONVERT-TRJ(1)                  GROMACS                 GMX-CONVERT-TRJ(1)
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NAME

6       gmx-convert-trj - Converts between different trajectory types
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SYNOPSIS

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

19       gmx  convert-trj  converts  trajectory files between different formats.
20       The module supports writing all GROMACS supported file formats from the
21       supported input formats.
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23       Included  is  also a selection of possible options to modify individual
24       trajectory frames, including options to produce slimmer  output  files.
25       It  is  also possible to replace the particle information stored in the
26       input trajectory with those from a structure file
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28       The module can also generate subsets of trajectories based on user sup‐
29       plied selections.
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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       Options to specify output files:
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46       -o [<.xtc/.trr/...>] (trajout.xtc)
47              Output trajectory: xtc trr cpt gro g96 pdb tng
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49       Other options:
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51       -b <time> (0)
52              First frame (ps) to read from trajectory
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54       -e <time> (0)
55              Last frame (ps) to read from trajectory
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57       -dt <time> (0)
58              Only use frame if t MOD dt == first time (ps)
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60       -tu <enum> (ps)
61              Unit for time values: fs, ps, ns, us, ms, s
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63       -fgroup <selection>
64              Atoms stored in the trajectory file (if not set, assume first  N
65              atoms)
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67       -xvg <enum> (xmgrace)
68              Plot formatting: xmgrace, xmgr, none
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70       -[no]rmpbc (yes)
71              Make molecules whole for each frame
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73       -[no]pbc (yes)
74              Use periodic boundary conditions for distance calculation
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76       -sf <file>
77              Provide selections from files
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79       -selrpos <enum> (atom)
80              Selection  reference positions: atom, res_com, res_cog, mol_com,
81              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
82              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
83              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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85       -select <selection>
86              Selection of particles to write to the file
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88       -vel <enum> (preserved-if-present)
89              Save velocities from frame  if  possible:  preserved-if-present,
90              always, never
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92       -force <enum> (preserved-if-present)
93              Save  forces  from  frame if possible: preserved-if-present, al‐
94              ways, never
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96       -atoms <enum> (preserved-if-present)
97              Decide on providing new atom information from topology or  using
98              current   frame   atom  information:  preserved-if-present,  al‐
99              ways-from-structure, never, always
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101       -precision <int> (3)
102              Set output precision to custom value
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104       -starttime <time> (0)
105              Change start time for first frame
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107       -timestep <time> (0)
108              Change time between different frames
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110       -box <vector>
111              New diagonal box vector for output frame
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SEE ALSO

114       gmx(1)
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116       More    information    about    GROMACS    is    available    at     <‐
117       http://www.gromacs.org/>.
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120       2022, GROMACS development team
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1252022.2                           Jun 16, 2022               GMX-CONVERT-TRJ(1)
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