[gmx-users] non-neutral system

Smith, Micholas D. smithmd at ornl.gov
Mon Nov 6 11:58:39 CET 2017

A requirement of PME is that the net charge is zero. Adding counter-ions would be considered standard-fare. Check out the paper:  https://www.unc.edu/~perera/PAPERS/JChemPhys_1995_103_8577.pdf for details (A smooth particle mesh Ewald method).

Best of luck

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 Faezeh Pousaneh <fpoosaneh at gmail.com>
Sent: Monday, November 06, 2017 5:50 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] non-neutral system


I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

Best regards
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