table of contents
g_traj(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_traj(1) |
NAME¶
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectorySYNOPSIS¶
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 realDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
xvgr/xmgr file
Trajectory: xtc trr trj gro g96 pdb cpt
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Protein data bank file
Protein data bank file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
Time unit: fs, ps, ns, us, ms or s
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Plot data for the com of each group
Make molecules whole for COM
Index contains molecule numbers iso atom numbers
Remove jumps of atoms across the box
Plot X-component
Plot Y-component
Plot Z-component
Number of groups to consider
Plot vector length
Full precision output
Binwidth for velocity histogram (nm/ps)
Use frame at this time for x in -cv and -cf instead of the average x
Scale factor for .pdb output, 0 is autoscale
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |