NAME
g_bundle - analyzes bundles of axes, e.g. helices
VERSION 4.0.1
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 -nice int -b time -e time -dt time -tu enum
-[no]xvgr -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
-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 or s
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-na int 0
Number of axes
-[no]zno
Use the Z-axis as reference iso the average axis
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_bundle(1)