g_bundle

| ## g_bundle Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### Description

g_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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-s` | `topol.tpr` | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-ol` | `bun_len.xvg` | Output | xvgr/xmgr file
`-od` | `bun_dist.xvg` | Output | xvgr/xmgr file
`-oz` | `bun_z.xvg` | Output | xvgr/xmgr file
`-ot` | `bun_tilt.xvg` | Output | xvgr/xmgr file
`-otr` | `bun_tiltr.xvg` | Output | xvgr/xmgr file
`-otl` | `bun_tiltl.xvg` | Output | xvgr/xmgr file
`-ok` | `bun_kink.xvg` | Output, Opt. | xvgr/xmgr file
`-okr` | `bun_kinkr.xvg` | Output, Opt. | xvgr/xmgr file
`-okl` | `bun_kinkl.xvg` | Output, Opt. | xvgr/xmgr file
`-oa` | `axes.pdb` | Output, Opt. | Protein data bank file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | gmx_bool | `no` | Print help info and quit
`-[no]version` | gmx_bool | `no` | Print version info and quit
`-nice` | int | `19` | Set the nicelevel
`-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` | Time unit: `fs`, `ps`, `ns`, `us`, `ms` or `s`
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-na` | int | `0` | Number of axes
`-[no]z` | gmx_bool | `no` | Use the Z-axis as reference iso the average axis

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