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)

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