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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                     GMX-BUNDLE(1)

gmxbundle 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 setaxistrue to display the reference axis.

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

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb 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

gmx(1)

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

          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]