g_traj_d (1) Linux Manual Page

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/>.