Re: vmd-l: counting gas molecules inside the nanotube

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 12:29:34 CDT

Hi,
  You could just as easily use a more complex equation for the radii,
or you could select all atoms within an oversized cylinder, and then
individually test and eliminate the ones falling outside of the precise
shape of your nanotube. If you don't have an equation for the shape
of your nanotube, you could probably use further atom selections to
find the bounds of the nanotube along a particular section and catch
the atoms on the interior that way. There may be a more elegant approach
for this sort of thing, but these ought to get you started.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 18, 2008 at 10:11:04PM +0500, Alexander A. Vakhrushev wrote:
> Hi John!
>
> Michael is my colleague so I'm little bit more informed about his
> task. He simulates complicated bottle-shaped carbon system, so
> alignment along one of axes is not the complete solution. Anticipating
> his subsequent question, how to extract atoms which are located inside
> volume limited by given (solid) surface?
>
> Thank you!
>
> 2008/9/18, John Stone <johns_at_ks.uiuc.edu>:
> >
> > Hi,
> > If the nanotube is aligned along one of the coordinate axes,
> > you can select all atoms within the tube using their x/y/z coordinates,
> > e.g.:
> > # for nanotube coaxial with Z coordinate axis
> > # assumes atom selection macro "gas" has been defined
> > set nanotuberadius 10
> > set withintube [atomselect top "gas and sqrt(x*x + y*y) < $nanotuberadius"]
> >
> > You'll need to replace "gas" with whatever atom name selection
> > applies for your system. Hope that helps.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Thu, Sep 18, 2008 at 03:52:51PM +0400, mishacat_at_udm.ru wrote:
> > > Hi everyone!
> > > Below my problem.
> > > I have a system - nanotube in gas. A few gas molecules penetrated into the tube and I need to count it.
> > > Any approaches of counting gas molecules inside the nanotube are welcome.
> > >
> > > --
> > > Sincerely yours,
> > > Mikhail Suyetin
> >
> > > ????????-450 512????/??? ?? 450 ??????!!! ????? ?????? ? ???????!!!
> >
> > > http://izhevsk.net/html/price.html
> >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> Best regards,
>
> Dr. Alexander Vakhrushev
> Institute of Applied Mechanics
> Dep. of Mech. and Phys.-Chem.
> of heterogeneous media
> UB of Russian Academy of Sciences
> 34 T. Baramzinoy St.
> Izhevsk, Russia 426067
> ----------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

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