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GMX-TRAJECTORY(1) GROMACS GMX-TRAJECTORY(1)

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: 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

SEE ALSO

gmx(1)
More information about GROMACS is available at < http://www.gromacs.org/>.

COPYRIGHT

2018, GROMACS development team
June 14, 2018 2018.2