g_traj(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 g_traj(1)

NAME

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

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       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

DESCRIPTION

	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  con-
       strained 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 trajec-
       tory 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 dis-
       tribution is given.

FILES

       -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

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	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

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

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

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

       -[no]pbcyes
	Make molecules whole for COM

       -[no]molno
	Index contains molecule numbers iso atom numbers

       -[no]nojumpno
	Remove jumps of atoms across the box

       -[no]xyes
	Plot X-component

       -[no]yyes
	Plot Y-component

       -[no]zyes
	Plot Z-component

       -ng int 1
	Number of groups to consider

       -[no]lenno
	Plot vector length

       -[no]fpno
	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

       gromacs(7)

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

								  Mon 4 Apr 2011							 g_traj(1)