NAME

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

       VERSION 4.6.5

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 2 Dec 2013                              g_bundle(1)