gmx trajectory#

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