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


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]


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 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



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2019, GROMACS development team
February 15, 2019 2019.1