Re: Thiol on gold simulation in NAMD

From: Axel Kohlmeyer (
Date: Wed Feb 25 2009 - 10:53:44 CST

On Wed, 25 Feb 2009, Jorgen Simonsen wrote:

JS> Hi,

hi jorgen,

JS> I was wondered a little bit about this subject as well - the parameters are
JS> probably not perfect but if ones would like to have just a qualitative
JS> understand of for example orientations of protein on a surface could the
JS> parameters from the following article not be used "Electronic Coupling
JS> Between Azurin and Gold at Different Protein/Substrate Orientations" by
JS> Venkat et al.>
JS> 1002/smll.200700001

the topic of this paper is _very_ different from the original
question, which was looking for a quantitative description of
lateral pulling forces of a thiol across a gold surface.

so there seem to be two different problems to consider:

a) how do sulfur and gold interact? and what reconstruction
happens on the surface near the bonding site? and what
happens if you try to drag the sufur around? this needs in
my opinion to be treated with ab initio MD. there are many
indications that you don't just move the sulfur around, but
rather have some gold atoms attached to it and if you try
to rupture the gold-sulfur bond that you'd actually have a
few gold atoms still attached to the sulfure and thus the
bond you break last would be a gold-gold bond and not a
gold-sulfur bond.

b) how does the gold-sulfur interaction affect the orientation
 of what is attached to the gold surface? since you do have
a strong _chemical_ gold-sulfur bond, there is good reason to
believe that this affects the orientation of what is bound to
the sulfur. for (small) thiols i would expect this to be much
more important than for a (large) protein.
but in the latter case, it would be hard to assess on the time
scales available to us from a simulation, how much of the orientating
effect does actually prevail and how much is determined from
the initial conditions.

the paper you quote actually mentions pending improvements to
the potentials used and the outcome of the study would be little
if any affected by any changes there. at least this is my personal


JS> Any comments would be very nice
JS> Thanks in advance
JS> best regards
JS> On Tue, Feb 17, 2009 at 9:54 PM, Axel Kohlmeyer <
JS> > wrote:
JS> > On Tue, 17 Feb 2009, S.K. Ghosh wrote:
JS> >
JS> > SKG> Dear users,
JS> > SKG>
JS> > SKG> I would like to know whether the following can be modelled using NAMD.
JS> > SKG>
JS> > SKG> A simple alkane thiol on gold. Wish to evaluate the lateral force at
JS> > which
JS> > SKG> the S atom (of the thiol) starts sliding/desorption on gold.
JS> > SKG>
JS> > SKG> Can we get Sulphur-Gold potential parameters?
JS> >
JS> > dear sourav,
JS> >
JS> > not for NAMD. not very soon.
JS> >
JS> > please have a look at:
JS> > and the PRL on methyl thiols referencend in it.
JS> >
JS> > there are people currently working on taking the results of
JS> > these - quite massive - calculations and turning them into
JS> > some analytical potential. people have done it before based
JS> > on gold clusters and a single thiol and the result was not
JS> > convincing. the resulting potential will have to be a manybody
JS> > potential, thus and i doubt that somebody would be willing to
JS> > implement it into NAMD, since there are codes around that are
JS> > more flexible (but slower!).
JS> >
JS> > SKG> The system would contain 2-3 layers of gold atoms, each layer with
JS> > around
JS> > SKG> 10 gold atoms. On top of gold layer around 5-6 thiols.
JS> >
JS> > you need more. the adsorption of thiols on gold is quite
JS> > complicated, you'd most likely be dragging some gold atoms
JS> > around attached to the sulphur of your thiol.
JS> >
JS> > cheers,
JS> > axel.
JS> >
JS> >
JS> > SKG> Your inputs would be very much valuable and appreciated.
JS> > SKG>
JS> > SKG> Thanks,
JS> > SKG> Sourav
JS> > SKG>
JS> > SKG>
JS> >
JS> > --
JS> > =======================================================================
JS> > Axel Kohlmeyer
JS> > Center for Molecular Modeling -- University of Pennsylvania
JS> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
JS> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
JS> > =======================================================================
JS> > If you make something idiot-proof, the universe creates a better idiot.
JS> >
JS> >

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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