From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 03 2014 - 15:49:35 CDT
On Tue, Jun 3, 2014 at 10:17 PM, Daniel Torrente <xlb608_at_my.utsa.edu> wrote:
> 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.
again, i think a "just give me the force field" kind of approach is going
to be successful here. there is much more literature and fundamental
research ahead of you before i would even begin any kind of simulation. you
first have to understand the chemistry of what you are looking at well
that will most likely require some level of ab initio or semi-empirical
calculation. using a subset of your total system to train and benchmark any
force field parameter set.
i would suspect that you still need some form of many-body potential, eg.
MEAM to represent Au atoms and study their clustering, which means you
would have to use an MD code that can handle multiple force field types at
the same time or supports (mechanical or better) coupling of codes.
> Daniel Torrente
> On Tue, Jun 3, 2014 at 2:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>> hi daniel,
>> On Tue, Jun 3, 2014 at 8:31 PM, Daniel Torrente <xlb608_at_my.utsa.edu>
>>> 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 akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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