Re: Thiol on gold simulation in NAMD

From: Axel Kohlmeyer (
Date: Tue Feb 17 2009 - 14:54:51 CST

On Tue, 17 Feb 2009, S.K. Ghosh wrote:

SKG> Dear users,
SKG> I would like to know whether the following can be modelled using NAMD.
SKG> A simple alkane thiol on gold. Wish to evaluate the lateral force at which
SKG> the S atom (of the thiol) starts sliding/desorption on gold.
SKG> Can we get Sulphur-Gold potential parameters?

dear sourav,

not for NAMD. not very soon.

please have a look at:
and the PRL on methyl thiols referencend in it.

there are people currently working on taking the results of
these - quite massive - calculations and turning them into
some analytical potential. people have done it before based
on gold clusters and a single thiol and the result was not
convincing. the resulting potential will have to be a manybody
potential, thus and i doubt that somebody would be willing to
implement it into NAMD, since there are codes around that are
more flexible (but slower!).

SKG> The system would contain 2-3 layers of gold atoms, each layer with around
SKG> 10 gold atoms. On top of gold layer around 5-6 thiols.

you need more. the adsorption of thiols on gold is quite
complicated, you'd most likely be dragging some gold atoms
around attached to the sulphur of your thiol.


SKG> Your inputs would be very much valuable and appreciated.
SKG> Thanks,
SKG> Sourav

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:22 CST