---
name: "gmx-bundle"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-bundle"
---

# gmx-bundle(1)

Analyze bundles of axes, e.g., helices

## 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)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team