man g_traj (Commandes) - g_traj VERSION 3.3_beta_20050823
NAME
g_traj VERSION 3.3_beta_20050823
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 -vd veldist.xvg -cv veloc.pdb -cf force.pdb -[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 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.
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 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
-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
OTHER OPTIONS
-[no]h no 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 , s , m or h
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[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
-ng int 1 Number of groups to consider
-[no]len no Plot vector length
-bin real 1 Binwidth for velocity histogram (nm/ps)
-scale real 0 Scale factor for pdb output, 0 is autoscale