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)