AMBER Archive (2006)

Subject: Re: AMBER: counterions and particle-mesh-ewald

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 30 2006 - 15:14:40 CDT

On Tue, Aug 29, 2006, cristian obiol wrote:
>
> I have performed some molecular dynamics without neutralizing the system ( no
> counterions ) and using periodic boundary conditions with particle-mesh-ewald
> method.
>
> It's correct a dynamics with PME and without counterions ??

There is no formal requirement that a PME simulation be neutral; if it is not,
there is an effective uniform "plasma" of charge that provides the
neutralization.

In principle, explicit counterions are a more physical representation of the
underlying reality. In practice, many (most?) simulations do not sample
enough to really average over all the energetically accessible counterion
configurations. In that case, using a plasma might actually be better than
using explicit counterions. I don't know that there is any general rule that
can be drawn here.

Others with good experience, or who have read the literature better than I
have, might chime in here.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu