Man page - gmx-bundle(1)
Packages contains this manual
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- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
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- gmx-densmap(1)
- gmx-rotacf(1)
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- gmx-hbond(1)
- gmx-rotmat(1)
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- gmx-rms(1)
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- gmx-rdf(1)
- gmx-pairdist(1)
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apt-get install gromacs-data
Manual
GMX-BUNDLE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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
gmx(1)
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2025, GROMACS development team