.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_bundle - analyzes bundles of axes, e.g. helices

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_bundle\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-ol" " bun_len.xvg "
.BI "\-od" " bun_dist.xvg "
.BI "\-oz" " bun_z.xvg "
.BI "\-ot" " bun_tilt.xvg "
.BI "\-otr" " bun_tiltr.xvg "
.BI "\-otl" " bun_tiltl.xvg "
.BI "\-ok" " bun_kink.xvg "
.BI "\-okr" " bun_kinkr.xvg "
.BI "\-okl" " bun_kinkl.xvg "
.BI "\-oa" " axes.pdb "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-xvg" " enum "
.BI "\-na" " int "
.BI "\-[no]z" ""
.SH DESCRIPTION
\&\fB g_bundle\fR analyzes bundles of axes. The axes can be for instance
\&helix axes. The program reads two index groups and divides both
\&of them in \fB \-na\fR parts. The centers of mass of these parts
\&define the tops and bottoms of the axes.
\&Several quantities are written to file:
\&the axis length, the distance and the z\-shift of the axis mid\-points
\&with respect to the average center of all axes, the total tilt,
\&the radial tilt and the lateral tilt with respect to the average axis.
\&


\&With options \fB \-ok\fR, \fB \-okr\fR and \fB \-okl\fR the total,
\&radial and lateral kinks of the axes are plotted. An extra index
\&group of kink atoms is required, which is also divided into \fB \-na\fR
\&parts. The kink angle is defined as the angle between the kink\-top and
\&the bottom\-kink vectors.
\&


\&With option \fB \-oa\fR the top, mid (or kink when \fB \-ok\fR is set)
\&and bottom points of each axis
\&are written to a \fB .pdb\fR file each frame. The residue numbers correspond
\&to the axis numbers. When viewing this file with Rasmol, use the
\&command line option \fB \-nmrpdb\fR, and type \fB set axis true\fR to
\&display the reference axis.
.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 "\-ol" " bun_len.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-od" " bun_dist.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-oz" " bun_z.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ot" " bun_tilt.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-otr" " bun_tiltr.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-otl" " bun_tiltl.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ok" " bun_kink.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-okr" " bun_kinkr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-okl" " bun_kinkl.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oa" " axes.pdb" 
.B Output, Opt.
 Protein data bank 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 "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-na"  " int" " 0" 
 Number of axes

.BI "\-[no]z"  "no    "
 Use the \fI z\fR\-axis as reference instead of the average axis

.SH SEE ALSO
.BR gromacs(7)

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