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/>.