Main Table of Contents

Thu 26 Aug 2010


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.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no Print version 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: fs, ps, ns, us, ms or s
-[no]w gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]com gmx_bool no Plot data for the com of each group
-[no]pbc gmx_bool yes Make molecules whole for COM
-[no]mol gmx_bool no Index contains molecule numbers iso atom numbers
-[no]nojump gmx_bool no Remove jumps of atoms across the box
-[no]x gmx_bool yes Plot X-component
-[no]y gmx_bool yes Plot Y-component
-[no]z gmx_bool yes Plot Z-component
-ng int 1 Number of groups to consider
-[no]len gmx_bool no Plot vector length
-[no]fp gmx_bool no Full precision output
-bin real 1 Binwidth for velocity histogram (nm/ps)
-scale real 0 Scale factor for pdb output, 0 is autoscale