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g_traj_d

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.