g_bundle(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_bundle(1)

NAME

       g_bundle - analyzes bundles of axes, e.g. helices

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_bundle  -f  traj.xtc  -s  topol.tpr  -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl
       bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -[no]version -nice int -b time -e  time  -dt  time
       -tu enum -xvg enum -na int -[no]z

DESCRIPTION

	g_bundle analyzes bundles of axes. The axes can be for instance helix axes. The program reads two index groups and divides both of them in
       -na 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  -ok,  -okr and  -okl 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  -na parts. The kink angle is defined as the angle between the kink-top and the bottom-kink vectors.

       With option  -oa the top, mid (or kink when  -ok is set) and bottom points of each axis are written to a  .pdb file each frame. The residue
       numbers correspond to the axis numbers. When viewing this file with Rasmol, use the command line option	-nmrpdb, and type  set	axis  true
       to display the reference axis.

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

       -ol bun_len.xvg Output
	xvgr/xmgr file

       -od bun_dist.xvg Output
	xvgr/xmgr file

       -oz bun_z.xvg Output
	xvgr/xmgr file

       -ot bun_tilt.xvg Output
	xvgr/xmgr file

       -otr bun_tiltr.xvg Output
	xvgr/xmgr file

       -otl bun_tiltl.xvg Output
	xvgr/xmgr file

       -ok bun_kink.xvg Output, Opt.
	xvgr/xmgr file

       -okr bun_kinkr.xvg Output, Opt.
	xvgr/xmgr file

       -okl bun_kinkl.xvg Output, Opt.
	xvgr/xmgr file

       -oa axes.pdb Output, Opt.
	Protein data bank file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -na int 0
	Number of axes

       -[no]zno
	Use the  z-axis as reference instead of the average axis

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_bundle(1)