Re: Thiol on gold simulation in NAMD

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 17 2009 - 14:54:51 CST

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

SKG> Dear users,
SKG>
SKG> I would like to know whether the following can be modelled using NAMD.
SKG>
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>
SKG> Can we get Sulphur-Gold potential parameters?

dear sourav,

not for NAMD. not very soon.

please have a look at: http://dx.doi.org/10.1126/science.1158532
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.

cheers,
   axel.

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

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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