Re: Thiol on gold simulation in NAMD

From: S.K. Ghosh (
Date: Wed Feb 18 2009 - 15:45:00 CST

Hi users,

Sorry - forgot to mark a copy to the group.


---------- Forwarded message ----------
Date: 18 Feb 2009 20:35:50 +0000
From: "S.K. Ghosh" <>
To: Axel Kohlmeyer <>
Subject: Re: namd-l: Thiol on gold simulation in NAMD

Hi Axel,

Thanks for getting back to me. I have gone through both the papers you
suggested and noted your following suggestion at the end of the 'Science'
paper: "this gives paramount importance to the development of empirical
potential models that include not only molecule-molecule interactions but
explicitly the Au-SR interactions"

Would you suggest then that it is not prudent now to try a molecular
simulation of thiol sliding on gold with empirical formula. I need to get
an idea of the parallel FORCE that initiates sliding of thiol on gold. The
only paper that seems to have attempted to do this is the following. But
the force of thiol rupture 1.5 nN (for parallel stretch) seems to be pretty
high. I certainly expect something less than 100 pN. Would you agree with

Density functional study of a typical thiol tethered on a gold surface:
ruptures under normal or parallel stretch

If you think that a molecular simulation may be tried, what would be a
suitable potential to use?

Would you suggest that I see whether its possible to do this simulation in
other package for e.g. LAMMPS, since I can't do that in NAMD?

Is there any way that I can make a good estimate of how much the force
would differ from the above paper without actually doing the simulation.

Your suggestion would be very helpful and much appreciated.


On Feb 17 2009, 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.
> axel.
>SKG> Your inputs would be very much valuable and appreciated.
>SKG> Thanks,
>SKG> Sourav

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