• ## Outreach

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Sep 19 2008 - 11:38:19 CDT

Hi guys,

What do you mean by "complicated bottle-shaped carbon system"?
is it a bunch of nanotubes or custom-shaped nanosystem?
2008/9/19 John Stone <johns_at_ks.uiuc.edu>

>
> 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!
> >
> > 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) <
> > >
> > > 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
> > ----------------------------------
> > ? ?????????,
> > ???????? ????????? ?????????????
> >
> > ?.?.-?.?., ?.?.?.
> > ???????? ?????????? ????????
> > ?????????? ?????????
> > ?????????? ???????? ????
> > 426067, ?. ??????
> > ??. ?. ?????????? 34
> > +7(3412)21-45-83
>
> --
> 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
>
>

```--
-Liu bo
-----------------------------------------------------------
Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
Chinese Academy of Sciences, Beijing P.R. China
Office: (86)-010-88233187
Home: (86)-010-88259765
Cell: 13426057875
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