AMBER Archive (2006)

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

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Aug 30 2006 - 17:59:32 CDT

I agree with dac on this
td

On Wed, 30 Aug 2006, David A. Case wrote:

> 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
>
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