g_traj(1)

NAME
g_traj VERSION 3.2.0

SYNOPSIS
g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -cv veloc.pdb -cf force.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]com -[no]mol -[no]nojump -[no]x -[no]y -[no]z -[no]len -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 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.

FILES
-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt.
 Index file -ox coord.xvg Output, Opt.
 xvgr/xmgr file -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 -cv veloc.pdb Output, Opt.
 Protein data bank file -cf force.pdb Output, Opt.
 Protein data bank file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -tu enum ps
 Time unit: ps , fs , ns , us , ms , s , m or h -[no]w no
 View output xvg, xpm, eps and pdb files -[no]com no
 Plot data for the com of each group -[no]mol no
 Index contains molecule numbers iso atom numbers -[no]nojump no
 Remove jumps of atoms across the box -[no]x yes
 Plot X-component -[no]y yes
 Plot Y-component -[no]z yes
 Plot Z-component -[no]len no
 Plot vector length -scale real 0
 Scale factor for pdb output, 0 is autoscale