NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a
trajectory
VERSION 4.0.1
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 -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
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. 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
-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
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]comno
Plot data for the com of each group
-[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
-bin real 1
Binwidth for velocity histogram (nm/ps)
-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/>.
Thu 16 Oct 2008 g_traj(1)