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