---
name: "g_bundle_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-bundle"
---

# g\_bundle\_d(1)

Analyze bundles of axes, e.g., helices

Part of [gmx-bundle(1)](/gmx-bundle/1.md).

## NAME

gmx-bundle - Analyze bundles of axes, e.g., helices

## SYNOPSIS

gmx bundle \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
            \[-n \[\<.ndx\>\]\] \[-ol \[\<.xvg\>\]\] \[-od \[\<.xvg\>\]\] \[-oz \[\<.xvg\>\]\]\
            \[-ot \[\<.xvg\>\]\] \[-otr \[\<.xvg\>\]\] \[-otl \[\<.xvg\>\]\]\
            \[-ok \[\<.xvg\>\]\] \[-okr \[\<.xvg\>\]\] \[-okl \[\<.xvg\>\]\]\
            \[-oa \[\<.pdb\>\]\] \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\]\
            \[-dt \<time\>\] \[-tu \<enum\>\] \[-xvg \<enum\>\] \[-na \<int\>\]\
            \[-\[no\]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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

**-ol** *\[\<.xvg\>\] (bun\_len.xvg) (Output)*\
     xvgr/xmgr file

**-od** *\[\<.xvg\>\] (bun\_dist.xvg) (Output)*\
     xvgr/xmgr file

**-oz** *\[\<.xvg\>\] (bun\_z.xvg) (Output)*\
     xvgr/xmgr file

**-ot** *\[\<.xvg\>\] (bun\_tilt.xvg) (Output)*\
     xvgr/xmgr file

**-otr** *\[\<.xvg\>\] (bun\_tiltr.xvg) (Output)*\
     xvgr/xmgr file

**-otl** *\[\<.xvg\>\] (bun\_tiltl.xvg) (Output)*\
     xvgr/xmgr file

**-ok** *\[\<.xvg\>\] (bun\_kink.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-okr** *\[\<.xvg\>\] (bun\_kinkr.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-okl** *\[\<.xvg\>\] (bun\_kinkl.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-oa** *\[\<.pdb\>\] (axes.pdb) (Output, Optional)*\
     Protein data bank file

Other options:

**-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, 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

**[gromacs(7)](/gromacs/7.md)**

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