Man page - gmx-trajectory(1)
Packages contains this manual
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apt-get install gromacs-data
Manual
GMX-TRAJECTORY
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-trajectory - Print coordinates, velocities, and/or forces for selections
SYNOPSIS
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
]
DESCRIPTION
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
SEE ALSO
gmx(1)
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COPYRIGHT
2025, GROMACS development team