[gmx-users] g_bundle question

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Hello,
> I am trying to calculate the tilt angle of the principal axis of a 
> nanotube inserted into a membrane using g_bundle. In the index file I 
> have selected a group of atoms at the top and a group of atoms at the 
> bottom of the nanotube, and I using the option -na 1 and -z to calculate 
> the tilt respect to the z axis of the membrane.
> I suppose that the results I have obtained in bun_tilt.xvg are the tilt 
> angles respect to the average axis (along the simulation), is that 
> right? Is there any way to calculate the tilt angle respect to a 
> reference axis (for example, the axis formed by the 2 groups in the 
> index file in the first structure, which is just perpendicular to the 
> membrane?

Sounds like something g_sgangle can do.

-Justin

> Thanks a lot in advance for your help.
> Best wishes,
> 
> Rebeca Garcia
> Santiago de Compostela University
> Spain
> regafan at hotmail.com
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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