From: Axel Kohlmeyer (
Date: Tue Dec 14 2010 - 04:21:44 CST

On Tue, Dec 14, 2010 at 4:38 AM, candy deck <> wrote:
> Hello,
> I'm working on the adsorption of dioxins into zeolite.
> I would like to know :
> 1. If there is a way to count the molecules adsorbed into the material

that depends on how you want to determine whether a molecule
is adsorbed or not. this is not a problem that VMD is commonly
used for, so you better familiarize yourself with VMD scripting first.

> 2. How to get the diffusion coefficient ? Does anybody has got a script that
> I can use?

that depends on whether you want to determine this from integrating
velocity auto-correlation functions or mean-squared displacement.
when analyzing a system with adsorption areas, you have to some
extra complications, that can invalidate the use of standard scripts
typically used to measure (self-)diffusion of molecules within (bulk)
liquids and solutions.

if you want to measure the diffusion through your zeolithe system,
you have measure the material flux through the solid area.
i would suggest you have a look in the vast amount of literature on
simulations of materials in zeolithes and see what others have done
and how they define relevant properties.

> Thanks
> Candy

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