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

[Smith, Micholas D.]

Thank you for correcting me Justin. I hadn't seen the old comment about the background plasma. And I should emphize, that I said it may not "nescessarily" result in problems, Justin is absolutely correct that if the system has even mild inhomogenties, artifacts will be produced.

-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 Justin Lemkul <jalemkul at vt.edu>
Sent: Wednesday, October 21, 2015 1:08 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] PME on a non-neutral system

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
>
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--
==================================================

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

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