Re: Ion Au+3 simulation

From: Axel Kohlmeyer (
Date: Tue Jun 03 2014 - 14:38:35 CDT

​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.


> Thanks in advance
> Daniel Torrente

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:49 CST