[gmx-users] PME on a non-neutral system

[Justin Lemkul]

On 10/21/15 12:14 PM, Smith, Micholas D. wrote:
> Albert,
>
> Gromacs won't automatically neutralize the system (as far as I know). If I recall being non-neutral doesn't necessarily result in problems, but may instead slow your run-time. I am sure someone will correct me if I am wrong.
>

Old posts suggest that GROMACS does in fact apply a neutralizing background plasma:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-April/020821.html

I suspect this is still the case.

Non-neutral systems can be problematic if they are inhomogeneous, e.g. a bilayer 
or something similar.  You can get big artifacts in those cases.

-Justin

> -Micholas
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Albert Solernou <a.solernou at leeds.ac.uk>
> Sent: Wednesday, October 21, 2015 11:14 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] PME on a non-neutral system
>
> Hi all,
> I accidentally rerun a trajectory that is not neutral, but that has a
> net charge of +2e. However, the system did not explode and the forces
> were not infinite, although I used PME. Is Gromacs neutralising the
> system automatically?
>
> Thanks,
> Albert
>
>
> --
> ---------------------------------
>     Dr Albert Solernou
>     EPSRC Research Fellow,
>     Department of Physics and Astronomy,
>     University of Leeds
>     Tel: +44 (0)1133 431451
>
> --
> 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.
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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