From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri May 18 2012 - 06:26:55 CDT

Dear Wendy,

You could calculate the "solvent accessible arrea" for every water
molecule (considering the solvent all the other waters).
Define a threshold for this and select those waters that are below this
threshold ..

If you have more cavities, you can do an additional step and select from
the selected waters those that are closed to the residues defining your
cavity of interest ...

Just an easy example ...
Vlad

On 05/18/2012 11:46 AM, Wendy González wrote:
> Dear VMD Users:
>
> I would like to calculate the amount of waters enclosed in an internal
> cavity of a protein during MD simulations.
> Do you have any tip?
> Thanks in advance,
> Wendy

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de