- bookworm 2022.5-2
- testing 2024.4-1
- unstable 2024.4-1
- experimental 2025.0~beta-1
GMX-BUNDLE(1) | GROMACS | GMX-BUNDLE(1) |
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¶
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2024, GROMACS development team
October 31, 2024 | 2024.4 |