[gmx-users] non-neutral system

[Justin Lemkul]

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 botching this up, but this is the conclusion I've withdrawn from reading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

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================