From: Daniel Torrente (xlb608_at_my.utsa.edu)
Date: Tue Jun 03 2014 - 16:17:38 CDT
Thanks again for your response, I will write back if I found a solution to
this.
Thanks
Daniel
On Tue, Jun 3, 2014 at 3:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>
> 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
> enough.
>
> 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.
>
> axel.
>
>
>
>>
>> Thanks
>>
>> 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>
>>> 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 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.
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:49 CST