gmx-trajectory - Print coordinates, velocities, and/or forces for selections

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                 GMX-TRAJECTORY(1)

gmxtrajectory  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.

       gmx-trajectory - Print coordinates, velocities, and/or forces for selections

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)(Optional)
              Input trajectory or single configuration: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Input structure: tprgrog96pdb 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

gmx(1)

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

          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]