[gmx-users] g_bundle question

[Rebeca García Fandiño]

OK,
you are right, I haven´t noticed the -z option! 
I will try it.
Thanks a lot for your help.
Best wishes,
Rebeca.

> Date: Thu, 16 Dec 2010 15:34:05 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_bundle question
> 
> 
> 
> 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
> 
> ========================================
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