[gmx-users] non-neutral system

Justin Lemkul jalemkul at vt.edu
Mon Nov 6 13:11:50 CET 2017

On 11/6/17 7:06 AM, João Henriques wrote:
> Hi Johannes,
> I just meant that from a purely theoretical point of view, it needs to be
> neutral. This has to do with the convergence of the outer infinite series,
> as the paper Micholas linked clearly states. I sincerely hope I'm not
> botching this up, but this is the conclusion I've withdrawn from reading
> the literature. Now, if the software implementation contains some tricks to
> account for this, that I'm not familiar with and will therefore leave that
> discussion for someone else more acquainted with it.

For your reference, it's explained in dx.doi.org/10.1021/ct400626b

All MD codes can do this when using PME, so it's not really a trick, 
just part of PME. It's not intuitive to most users, and not appropriate 
in many cases, hence the standard advice of "add counterions."



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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