gmx-trajectory1
Print coordinates, velocities, and/or forces for selections
Usage
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]
Overview
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
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
|
Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng |
|---|---|
-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
|
Input structure: tpr gro g96 pdb brk ent |
-n [<.ndx>] (index.ndx) (Optional)
|
Extra index groups |
Options to specify output files:
-ox [<.xvg>] (coord.xvg) (Optional)
|
Coordinates for each position as a function of time |
|---|---|
-ov [<.xvg>] (veloc.xvg) (Optional)
|
Velocities for each position as a function of time |
-of [<.xvg>] (force.xvg) (Optional)
|
Forces for each position as a function of time |
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
- -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 |
Releases
4 releases since Debian 10 (Buster); the text changed 3 times.