Provided by: gromacs-data_2019.3-2_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/>.

COPYRIGHT

       2019, GROMACS development team