From: Axel Kohlmeyer (
Date: Mon Jun 23 2008 - 10:11:04 CDT

On Mon, 23 Jun 2008, Anneta Tzampazi wrote:

AI> I am an MSc student trying to work on my thesis, involving molecular
AI> simulation of protein adsorption on thin layers. Since I have not been able
AI> to find any information about the parameters I need in order to model the
AI> crystal surfaces (graphite, ZnO or BN) for my simulation to begin, I am
AI> wondering whether this information is somewhere to be found (internet,
AI> bibliography, etc). In addition, I am interested in learning whether the

there have to be some studies on the various surfaces and thus
people will have published papers on it. to model the surfaces,
you may need to somewhat "freeze" atoms to their positions, as
i would be surprised if you can construct a classical model that,
e.g., can reproduce a ZnO surface well. graphite might be the
easiest, if you stick to a single graphene layer and don't need
the polarizability of larger graphite stacks. many of those
systems are studied with quantum chemistry methods to determine
their surface behavior. of course, the next problem would be to
parameterize the interaction with water and the amino acids...

AI> version of VMD for either Linux or Windows operating system can support the
AI> plugin of "Inorganic Builder" because I have not succeeded in running it via
AI> the VMD Tk console. Thank you in advance.

please take note that it is next to impossible to help somebody
reporting "it does not work". please explain in more detail what
you tried and what you expected to get and didn't and what you
got instead.


AI> Yours sincerely,
AI> Tzampazi Anneta

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.