AMBER Archive (2006)

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

From: Eric Hu (list.eric_at_gmail.com)
Date: Wed Oct 11 2006 - 18:37:01 CDT

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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