[gmx-users] g_bundle question

[Rebeca García Fandiño]

Thanks for the suggestion.
However, I have one question. If I use g_sgangle I can calculate the angle formed by the atoms at the top and bottom of my nanotube, but if the nanotube is considered as a whole (as a rigid system), and it tilts, then the result would not show the tilt respect to the z axis of the membrane, am I right? 
Thanks a lot for your help.
Best wishes,
Rebeca.

> Date: Thu, 16 Dec 2010 11:59:38 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_bundle question
> 
> 
> 
> 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
> > 
> 
> -- 
> ========================================
> 
> 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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