Scroll to navigation



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:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
xvg plot formatting: xmgrace, xmgr, none
Number of axes
-[no]z (no)
Use the z-axis as reference instead of the average axis



More information about GROMACS is available at <>.


2022, GROMACS development team

June 16, 2022 2022.2