From: meisam valizadeh kiamahalleh (
Date: Thu Jun 28 2012 - 05:38:45 CDT

Dear Fariba
Glad to hear your helpful reply on this matter. May I know if you have any
TCl script for calculating the water molecule's number over the simulation
time and a distance from the surface? I guess the suggestion that you made
 here is for finding the number of water molecule at a specific time, if I
am not mistaken.
I would be very grateful if you could share your experience with us.

On Thu, Jun 28, 2012 at 3:39 PM, fariba taghavi <> wrote:

> Dear Albert,
> Actually you can not find this option directly in the VMD but, you can
> use TLC to write a short code. My suggestion is to select oxygen atom
> in the hole (for example by "atomselect" to choose oxygen atoms with
> x^2+y^2+Z^2<=16, it is related to the shape of the hole) and then you
> can get the number of your selected atoms.
> Good Luck,
> Fariba Taghavi
> PhD Candidate in Physical Chemistry
> Tarbiat Modares University
> On 6/27/12, Albert <> wrote:
> > hello:
> >
> > I've finished a MD and I would like to to make statistics for the
> > water density in the 'hole' within the protein at specific region. I am
> > wondering, is it possible for VMD to do so ? Does anybody have any
> > suggestions? I've searched in the mailist and VMD plug-in/scripts pages,
> > but didn't find anything related.
> >
> > thank you very much
> > Albert
> >