AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 11 2006 - 11:16:23 CDT

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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