VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 11:18:43 CDT

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