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gmx-bundle - Online in the Cloud

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This is the command gmx-bundle that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum>
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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