Re: Thiol on gold simulation in NAMD

From: Jorgen Simonsen (
Date: Wed Feb 25 2009 - 04:36:47 CST


I was wondered a little bit about this subject as well - the parameters are
probably not perfect but if ones would like to have just a qualitative
understand of for example orientations of protein on a surface could the
parameters from the following article not be used "Electronic Coupling
Between Azurin and Gold at Different Protein/Substrate Orientations" by
Venkat et al.>

Any comments would be very nice

Thanks in advance

best regards


On Tue, Feb 17, 2009 at 9:54 PM, Axel Kohlmeyer <
> wrote:

> 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:
> 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>
> --
> =======================================================================
> 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.

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