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

Smith, Micholas D. smithmd at ornl.gov
Wed Oct 21 18:14:43 CEST 2015


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.


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?


   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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