.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_traj\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-ox" " coord.xvg "
.BI "\-oxt" " coord.xtc "
.BI "\-ov" " veloc.xvg "
.BI "\-of" " force.xvg "
.BI "\-ob" " box.xvg "
.BI "\-ot" " temp.xvg "
.BI "\-ekt" " ektrans.xvg "
.BI "\-ekr" " ekrot.xvg "
.BI "\-vd" " veldist.xvg "
.BI "\-cv" " veloc.pdb "
.BI "\-cf" " force.pdb "
.BI "\-av" " all_veloc.xvg "
.BI "\-af" " all_force.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]com" ""
.BI "\-[no]pbc" ""
.BI "\-[no]mol" ""
.BI "\-[no]nojump" ""
.BI "\-[no]x" ""
.BI "\-[no]y" ""
.BI "\-[no]z" ""
.BI "\-ng" " int "
.BI "\-[no]len" ""
.BI "\-[no]fp" ""
.BI "\-bin" " real "
.BI "\-ctime" " real "
.BI "\-scale" " real "
.SH DESCRIPTION
\&\fB g_traj\fR plots coordinates, velocities, forces and/or the box.
\&With \fB \-com\fR the coordinates, velocities and forces are
\&calculated for the center of mass of each group.
\&When \fB \-mol\fR is set, the numbers in the index file are
\&interpreted as molecule numbers and the same procedure as with
\&\fB \-com\fR is used for each molecule.


\&Option \fB \-ot\fR 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 \fB \-com\fR.


\&Options \fB \-ekt\fR and \fB \-ekr\fR plot the translational and
\&rotational kinetic energy of each group,
\&provided velocities are present in the trajectory file.
\&This implies \fB \-com\fR.


\&Options \fB \-cv\fR and \fB \-cf\fR write the average velocities
\&and average forces as temperature factors to a \fB .pdb\fR file with
\&the average coordinates or the coordinates at \fB \-ctime\fR.
\&The temperature factors are scaled such that the maximum is 10.
\&The scaling can be changed with the option \fB \-scale\fR.
\&To get the velocities or forces of one
\&frame set both \fB \-b\fR and \fB \-e\fR to the time of
\&desired frame. When averaging over frames you might need to use
\&the \fB \-nojump\fR 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 \fB .xvg\fR file as well
\&(specified with \fB \-av\fR or \fB \-af\fR).


\&Option \fB \-vd\fR 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.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-ox" " coord.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oxt" " coord.xtc" 
.B Output, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-ov" " veloc.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-of" " force.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ob" " box.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ot" " temp.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ekt" " ektrans.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ekr" " ekrot.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-vd" " veldist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cv" " veloc.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-cf" " force.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-av" " all_veloc.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-af" " all_force.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]com"  "no    "
 Plot data for the com of each group

.BI "\-[no]pbc"  "yes   "
 Make molecules whole for COM

.BI "\-[no]mol"  "no    "
 Index contains molecule numbers iso atom numbers

.BI "\-[no]nojump"  "no    "
 Remove jumps of atoms across the box

.BI "\-[no]x"  "yes   "
 Plot X\-component

.BI "\-[no]y"  "yes   "
 Plot Y\-component

.BI "\-[no]z"  "yes   "
 Plot Z\-component

.BI "\-ng"  " int" " 1" 
 Number of groups to consider

.BI "\-[no]len"  "no    "
 Plot vector length

.BI "\-[no]fp"  "no    "
 Full precision output

.BI "\-bin"  " real" " 1     " 
 Binwidth for velocity histogram (nm/ps)

.BI "\-ctime"  " real" " \-1    " 
 Use frame at this time for x in \fB \-cv\fR and \fB \-cf\fR instead of the average x

.BI "\-scale"  " real" " 0     " 
 Scale factor for \fB .pdb\fR output, 0 is autoscale

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.