g_traj(1)
NAME
g_traj - plots x, v, f, box, temperature and rotational energy from a
trajectory
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 . 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.
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
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.