[gmx-users] non-neutral system
joao.m.a.henriques at gmail.com
Mon Nov 6 13:15:55 CET 2017
Understood. Thank you Justin.
On Mon, Nov 6, 2017 at 1:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 botching this up, but this is the conclusion I've withdrawn from reading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
>> 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
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users