VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2011 - 13:59:40 CDT

Hi,
  I think you'll want to read the VMD Tutorials or the VMD User's Guide
to learn how to select atoms by their cartesian coordinates, so that you
can compute the atoms that are within your nanotube, and then use that
to write the necessary analysis script for your purposes:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node93.html

Cheers,
  John

On Tue, Sep 13, 2011 at 11:18:48AM +0800, meisam valizadeh kiamahalleh wrote:
> Dear VMD users
> I have run MD on carbon nanotube with solvated drug molecules inside and
> outside the tubes. Kindly would you please let me know how I
> can visualize and calculate the amount of molecules only inside the carbon
> nanotube during MD process. May I know what keywords I should use in graph
> presentation?
> Thank you very much
> Kind regards
> Meisam 

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