Provided by: gromacs-data_2020.1-1_all bug

NAME
       gmx-traj - Plot x, v, f, box, temperature and rotational energy from trajectories


SYNOPSIS
          gmx traj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                   [-ox [<.xvg>]] [-oxt [<.xtc/.trr/...>]] [-ov [<.xvg>]]
                   [-of [<.xvg>]] [-ob [<.xvg>]] [-ot [<.xvg>]] [-ekt [<.xvg>]]
                   [-ekr [<.xvg>]] [-vd [<.xvg>]] [-cv [<.pdb>]] [-cf [<.pdb>]]
                   [-av [<.xvg>]] [-af [<.xvg>]] [-b <time>] [-e <time>]
                   [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]com]
                   [-[no]pbc] [-[no]mol] [-[no]nojump] [-[no]x] [-[no]y]
                   [-[no]z] [-ng <int>] [-[no]len] [-[no]fp] [-bin <real>]
                   [-ctime <real>] [-scale <real>]


DESCRIPTION
       gmx traj plots coordinates, velocities, forces and/or the box.  With -com the coordinates, velocities and
       forces are calculated for the center of mass of each group.  When -mol is set, the numbers in  the  index
       file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule.

       Option  -ot  plots the temperature of each group, provided velocities are present in the trajectory file.
       No corrections are made for constrained degrees of freedom!  This implies -com.

       Options -ekt and -ekr plot the translational and  rotational  kinetic  energy  of  each  group,  provided
       velocities are present in the trajectory file.  This implies -com.

       Options -cv and -cf write the average velocities and average forces as temperature factors to a .pdb file
       with the average coordinates or the coordinates at -ctime.  The temperature factors are scaled such  that
       the  maximum  is 10.  The scaling can be changed with the option -scale.  To get the velocities or forces
       of one frame set both -b and -e to the time of desired frame. When averaging over frames you  might  need
       to  use  the  -nojump  option  to  obtain the correct average coordinates.  If you select either of these
       option the average force and velocity for each atom are written to an .xvg file as well  (specified  with
       -av or -af).

       Option  -vd  computes a velocity distribution, i.e. the norm of the vector is plotted. In addition in the
       same graph the kinetic energy distribution is given.

       See gmx trajectory for plotting similar data for selections.


OPTIONS
       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -ox [<.xvg>] (coord.xvg) (Optional)
              xvgr/xmgr file

       -oxt [<.xtc/.trr/...>] (coord.xtc) (Optional)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -ov [<.xvg>] (veloc.xvg) (Optional)
              xvgr/xmgr file

       -of [<.xvg>] (force.xvg) (Optional)
              xvgr/xmgr file

       -ob [<.xvg>] (box.xvg) (Optional)
              xvgr/xmgr file

       -ot [<.xvg>] (temp.xvg) (Optional)
              xvgr/xmgr file

       -ekt [<.xvg>] (ektrans.xvg) (Optional)
              xvgr/xmgr file

       -ekr [<.xvg>] (ekrot.xvg) (Optional)
              xvgr/xmgr file

       -vd [<.xvg>] (veldist.xvg) (Optional)
              xvgr/xmgr file

       -cv [<.pdb>] (veloc.pdb) (Optional)
              Protein data bank file

       -cf [<.pdb>] (force.pdb) (Optional)
              Protein data bank file

       -av [<.xvg>] (all_veloc.xvg) (Optional)
              xvgr/xmgr file

       -af [<.xvg>] (all_force.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]com (no)
              Plot data for the com of each group

       -[no]pbc (yes)
              Make molecules whole for COM

       -[no]mol (no)
              Index contains molecule numbers instead of atom numbers

       -[no]nojump (no)
              Remove jumps of atoms across the box

       -[no]x (yes)
              Plot X-component

       -[no]y (yes)
              Plot Y-component

       -[no]z (yes)
              Plot Z-component

       -ng <int> (1)
              Number of groups to consider

       -[no]len (no)
              Plot vector length

       -[no]fp (no)
              Full precision output

       -bin <real> (1)
              Binwidth for velocity histogram (nm/ps)

       -ctime <real> (-1)
              Use frame at this time for x in -cv and -cf instead of the average x

       -scale <real> (0)
              Scale factor for .pdb output, 0 is autoscale


SEE ALSO
       gmx(1)

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


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