NAME

       gmx-bundle - Analyze bundles of axes, e.g., helices

SYNOPSIS

          gmx bundle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                     [-ol [<.xvg>]] [-od [<.xvg>]] [-oz [<.xvg>]]
                     [-ot [<.xvg>]] [-otr [<.xvg>]] [-otl [<.xvg>]]
                     [-ok [<.xvg>]] [-okr [<.xvg>]] [-okl [<.xvg>]]
                     [-oa [<.pdb>]] [-b <time>] [-e <time>] [-dt <time>]
                     [-tu <enum>] [-xvg <enum>] [-na <int>] [-[no]z]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -ol [<.xvg>] (bun_len.xvg)
              xvgr/xmgr file

       -od [<.xvg>] (bun_dist.xvg)
              xvgr/xmgr file

       -oz [<.xvg>] (bun_z.xvg)
              xvgr/xmgr file

       -ot [<.xvg>] (bun_tilt.xvg)
              xvgr/xmgr file

       -otr [<.xvg>] (bun_tiltr.xvg)
              xvgr/xmgr file

       -otl [<.xvg>] (bun_tiltl.xvg)
              xvgr/xmgr file

       -ok [<.xvg>] (bun_kink.xvg) (Optional)
              xvgr/xmgr file

       -okr [<.xvg>] (bun_kinkr.xvg) (Optional)
              xvgr/xmgr file

       -okl [<.xvg>] (bun_kinkl.xvg) (Optional)
              xvgr/xmgr file

       -oa [<.pdb>] (axes.pdb) (Optional)
              Protein data bank file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -na <int> (0)
              Number of axes

       -[no]z (no)
              Use the z-axis as reference instead of the average axis

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2024, GROMACS development team