[gmx-users] g_bundle question

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> 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?

Maybe I'm not clear on what you want.  I haven't used g_sgangle much, but it 
seems to me that option -oa ("Angle between the two groups specified in the 
index file") would do what you want.  Otherwise, g_sgangle -z might.

-Justin

> 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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-- 
========================================

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

========================================