Hi Dac,
Thank you for your reply. I have thought of trying to extend the code to
add the extra points in CN-. I guess I will need a little guideline from
you regarding the codes.
Is it possible to add the extra point stuff in ff03 forcefield? Or, I have
to use the polarizable force fields only.
Surma Talapatra
Graduate Student
Geva Group
University of Michigan
On Tue, 28 Jun 2011 16:24:48 -0400, "David A. Case"
<case.biomaps.rutgers.edu> wrote:
> On Tue, Jun 28, 2011, tsurma.umich.edu wrote:
>>
>> I was wondering if you could give me an idea of how to add two extra
>> points
>> around the C atom in CN- ion. In polarizable force fields it adds
>>
>> "Epol = −2Σμi ·Eio"
>>
>> where the dipole moment is induced dipole moment.
>> I was trying to add a similar term with a 'permanent' dipole moment
>> around
>> C atom in a simulation of CN- in H2O.
>
> The extra point code is specialized to particular cases that arise in
> proteins
> and nucleic acids and water models. To make it a lot more general would
> require grokking the existing program and extending it. See:
>
> http://archive.ambermd.org/201104/0706.html
>
> ....dac
>
>
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Received on Thu Jun 30 2011 - 09:30:03 PDT
