gmx-trajectory - Print coordinates, velocities, and/or forces for
selections
gmx trajectory [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
[-n [<.ndx>]] [-ox [<.xvg>]] [-ov [<.xvg>]]
[-of [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
[-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
[-seltype <enum>] [-select <selection>] [-[no]x]
[-[no]y] [-[no]z] [-[no]len]
gmx trajectory plots coordinates, velocities, and/or forces
for provided selections. By default, the X, Y, and Z components for the
requested vectors are plotted, but specifying one or more of -len,
-x, -y, and -z overrides this.
For dynamic selections, currently the values are written out for
all positions that the selection could select.
Options to specify input files:
Options to specify output files:
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: none, xmgrace, xmgr
- -[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
- -seltype
<enum> (atom)
- Default selection output 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>
- Selections to analyze
- -[no]x (yes)
- Plot X component
- -[no]y (yes)
- Plot Y component
- -[no]z (yes)
- Plot Z component
- -[no]len (no)
- Plot vector length
gmx(1)
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