From: Axel Kohlmeyer (
Date: Tue Sep 13 2011 - 23:54:39 CDT

On Tue, Sep 13, 2011 at 11:23 PM, 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?

there is no single command that will do all you want
in a magic way. programs like VMD are no mindreaders.
all the do is provide a toolkit that _you_ will have to
utilize by determining how you translate "in the nanotube"
into terms that can be expressed by the available tools.

have a closer look at the VMD users guide and the tutorials.
there are many examples.


> Thank you very much
> Kind regards
> Meisam

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.