Man Linux: Main Page and Category List


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

       VERSION 4.0.1


       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 -nice int -b time -e time
       -dt time -tu enum -[no]w -[no]xvgr -[no]com -[no]mol -[no]nojump -[no]x
       -[no]y -[no]z -ng int -[no]len -bin 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.  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

       -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:  ps,  fs,  ns,  us,  ms or  s

        View output xvg, xpm, eps and pdb files

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        Plot data for the com of each group

        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

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

       -scale real 0
        Scale factor for pdb output, 0 is autoscale



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                      g_traj(1)