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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 bot- toms of the axes. Several quantities are written to file: the axis length, the distance and the z-shift of the axis mid-points with re- spect 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 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-BUNDLE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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