VMD-L Mailing List

From: Alexander A. Vakhrushev (makaveli.lcf_at_gmail.com)
Date: Thu Sep 18 2008 - 12:11:04 CDT

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
----------------------------------
С уважением,
    Вахрушев Александр Александрович
к.ф.-м.н., с.н.с.
Институт прикладной механики
Уральского Отделения
Российской Академии Наук
426067, г. Ижевск
ул. Т. Барамзиной 34
+7(3412)21-45-83