AMBER Archive (2005)

Subject: Re: AMBER: PB dynamics

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 12 2005 - 11:26:19 CST

On Wed, Jan 12, 2005, Nelson Fonseca wrote:
>
> Im interested in performing a MD simulation where the
> point key is to understand the effect of the solvent
> molecules ( n-hexane) in the stability between two
> complexes. I would like to know if the PB dynamics is
> suitable for this kind of problem. I have solvated my
> molecules with the option "solvatecap" in Xleap with the
> n-hexane solvent. Can I carry out the PB dynamics with the
> option igb=10 in sander and seting the value of the
> external dielectric constant equal to the experimental
> value for n-hexane?

This sounds OK, but you might find better and faster results by setting
up a periodic box simulation. You'd have to run some experiments to see
which looked better. Generally, reaction field models have been tested mostly
on high dielectric environments (like water).

...good luck...dac

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