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gmx-convert-trj

Converts between different trajectory types

gmx convert-trj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
             [-n [<.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>]


gmx convert-trj converts trajectory files between different formats. The module supports writing all GROMACS supported file formats from the supported input formats.

Included is also a selection of possible options to modify individual trajectory frames, including options to produce slimmer output files. It is also possible to replace the particle information stored in the input trajectory with those from a structure file

The module can also generate subsets of trajectories based on user supplied selections.

Options to specify input files:

Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
Input structure: tpr gro g96 pdb brk ent
Extra index groups

Options to specify output files:

Output trajectory: xtc trr cpt gro g96 pdb tng

Other options:

First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
Provide selections from files
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
Selection of particles to write to the file
Save velocities from frame if possible: preserved-if-present, always, never
Save forces from frame if possible: preserved-if-present, always, never
Decide on providing new atom information from topology or using current frame atom information: preserved-if-present, always-from-structure, never, always
Set output precision to custom value
Change start time for first frame
Change time between different frames
New diagonal box vector for output frame

gmx(1)

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