AMBER Archive (2006)

Subject: Re: AMBER: generalized born model for organic solvent

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Oct 11 2006 - 19:11:33 CDT

Eric (and all),
My understanding is that gb as parametrized in amber only for water.
There are no parameters out there for other solvents, but I would like
to know if I am wrong.

Now: after that is said, there is a flag in gb called extdiel. It should
be set to whatever your own solvent is. But, this still does not solve
the parameters problem. I do not know if anyone has studied this
carefully enough.

Alexey Onufriev has 'new' versions of gb using a slightly different
formalism, using parameters that should not depend on parameters for a
particular solvent. He has published these methods in the last couple of
years.

Cheers
Adrian

Eric Hu wrote:
> Dr. Case
> Based on your experience, can you recommend a set of parameters to use
> in that case? Thank you.
>
> -Eric
>
> On 10/11/06, David A. Case <case_at_scripps.edu> wrote:
>> On Tue, Oct 10, 2006, Eric Hu wrote:
>> >
>> > I want to speed up my simulation with explicit organic solvent
>> > (acetonitrile) model. Therefore I wonder if using implicit model might
>> > accelerate the simulation significantly. And is there anyway to
>> > introduce a GB model for any solvent in amber 9?
>>
>> GB has not been explicitly parameterized for acetonitrile, but might work
>> work reasonably well (since this solvent has a fairly high dielectric
>> constant). Whether or not you will see any speedups depends on the
>> size of
>> the system and other input parameters -- why not just try and find out
>> for
>> yourself?
>>
>> ...dac
>>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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