[gmx-users] g_bundle: angle with x or y axis.

[Justin Lemkul]

On 1/18/13 7:09 PM, Mortuza Munna wrote:
> Dear gromacs user,
> I have found that g_bundle can measure the angle between a group from
> index file and z-axis with the option -z. Is it possible to measure the angle of that group from index file with y-axis/x-axis? Any suggestion will be appreciable.
>

You cannot do this directly with g_bundle without modifying the source code to 
implement such functionality.

One approach would be to:

1. Use trjconv -sep to split your trajectory into individual frames (.pdb or .gro)
2. Rotate each frame to realign what was previously x or y with the z-axis.
3. Concatenate the frames with trjcat into a new trajectory
4. Apply g_bundle -z

The above approach can easily be scripted.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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