Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory
VERSION 4.6.5
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 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.
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 2 Dec 2013 g_traj(1)