AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 19 2007 - 19:01:00 CST

On Wed, Dec 19, 2007, Chris Moth wrote:

> > Does a simulation need to be charge equilibrated?
> >
> > I am running some MD simulations with my total charge equals -4
>
> That should not work well in a periodic box. It certainly would seem to
> be at least unphysical to simulate infinitely repeating, negatively
> charged boxes.

So it would seem, but Amber does not in fact simulate an infinite array of
negatively charged boxes. Rather, a uniform "plasma" of charge effectively
neutralizes all periodic systems. This, in turn, is not really "physical",
but also does not require the simulation to converge the locations of discrete
counterions. My guess is that in a blind test, one would be hard pressed to
discern whether counterions or a neutralizing plasma had been used, especially
if the total charge is relatively small, as it is here.

...dac

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