Re: Ion Au+3 simulation

From: Daniel Torrente (
Date: Tue Jun 03 2014 - 15:17:15 CDT

Thanks for your quick response

I will take your advice and keep looking for published literature on this
topic. In the mean time, if I tried to use Au+ or Au instead of Au3+, is
there any ff available that could help to carried out this simulation?.
Basically, I do not want to fix the Au atom. I want them to move freely
during the simulation and see the aggregation pattern over the surface of
the protein.


Daniel Torrente

On Tue, Jun 3, 2014 at 2:38 PM, Axel Kohlmeyer <> wrote:

> ​hi daniel,​
> On Tue, Jun 3, 2014 at 8:31 PM, Daniel Torrente <>
> wrote:
>> Hi guys,
>> Is there any available force field that can simulated the interaction
>> between Au+3 and a protein? I was looking for some information in articles
>> and the mailing list related to this topics, but all I could find was the
>> GoiP and GoiP-charmm (immobile surface Au). Also found the charmm-metal ff
>> but it seems that only works with the metal Au and not with the ion Au+3
>> (there is no information in the ff about Au+3).
>> Any suggestion on how to approach this type of interaction? or or could I
>> do this with any of the ff that I mentioned before?
> ​multiply charged ions are very problematic for pair-wise additive force
> fields as their interactions usually include polarization of the immediate
> environment with charge redistribution and directional interactions. most
> likely you will not have a "naked" au3+ cation, but some kind of complex
> with nulcleophilic molecules and/or anions. depending of what you want to
> study, you may need to resolve to doing QM/MM calculations​, or
> parameterize an au3+ complex that you keep rigid or otherwise maintain its
> charge distribution.
> interactions with gold surfaces are a different system, since those are
> usually dominated by a mostly covalent bond (via sulphur or oxygen) and the
> effects due to polarization of the metal are smaller than other errors of
> the model to be justifiably ignored. often people use rather crude models
> for it, since they don't care as much about the interaction with the gold
> surface than of the objects attached to the surface with each other and the
> items around it.
> ​i suggest you​ have another look at the published literature and think
> carefully what it is that you really want to learn from your simulations
> and come back, if you still have questions.
> also, please don't just take a single opinion on the subject as your
> guideline. for anything this problematic, you have to look at multiple
> contrasting opinions and form your own opinion as there is no single simple
> answer that answers all problems.
> axel.
>> Thanks in advance
>> Daniel Torrente
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

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