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

       VERSION 4.0.1


       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


       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.


       -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


        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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -na int 0
        Number of axes

        Use the Z-axis as reference iso the average axis



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                    g_bundle(1)