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

Groenhof, Gerrit ggroenh at gwdg.de
Wed Oct 21 21:30:25 CEST 2015


> 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.

yes, and it is not just gromacs, but inherent to Ewald sum methods. It is simply a consequence of leaving out the k=0 term in the reciprokal part.

> 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.

Indeed, see for example https://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf  for a description and explanation of the artefacts.

However, you wrote you want to do a -rerun. In that case, if the trajectory was generated with counter ions, there may be no problems.

> -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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