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GMX-TRAJECTORY(1) GROMACS GMX-TRAJECTORY(1) NAME gmx-trajectory - Print coordinates, velocities, and/or forces for se- lections 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 pro- vided selections. By default, the X, Y, and Z components for the re- quested 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) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-TRAJECTORY(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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