Provided by: gromacs-data_4.6.5-1build1_all bug


       g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory

       VERSION 4.6.5


       g_traj  -f  traj.xtc  -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg
       -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv
       veloc.pdb  -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -[no]version -nice int
       -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


        g_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.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -ox coord.xvg Output, Opt.
        xvgr/xmgr file

       -oxt coord.xtc Output, Opt.
        Trajectory: xtc trr trj gro g96 pdb cpt

       -ov veloc.xvg Output, Opt.
        xvgr/xmgr file

       -of force.xvg Output, Opt.
        xvgr/xmgr file

       -ob box.xvg Output, Opt.
        xvgr/xmgr file

       -ot temp.xvg Output, Opt.
        xvgr/xmgr file

       -ekt ektrans.xvg Output, Opt.
        xvgr/xmgr file

       -ekr ekrot.xvg Output, Opt.
        xvgr/xmgr file

       -vd veldist.xvg Output, Opt.
        xvgr/xmgr file

       -cv veloc.pdb Output, Opt.
        Protein data bank file

       -cf force.pdb Output, Opt.
        Protein data bank file

       -av all_veloc.xvg Output, Opt.
        xvgr/xmgr file

       -af all_force.xvg Output, Opt.
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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 when t MOD dt = first time (ps)

       -tu enum ps
        Time unit:  fs,  ps,  ns,  us,  ms or  s

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

        Plot data for the com of each group

        Make molecules whole for COM

        Index contains molecule numbers iso atom numbers

        Remove jumps of atoms across the box

        Plot X-component

        Plot Y-component

        Plot Z-component

       -ng int 1
        Number of groups to consider

        Plot vector length

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_traj(1)