Re: PME and net charge in the system

From: Chris Harrison (
Date: Thu Oct 27 2011 - 12:12:46 CDT


A charge nullifying correction is applied to periodic PME simulations,
conceptually like an inverse charge nullifying field.

It is however better to balance the charge in your system with solvated
ions, as the nullification correction is only an approximation.
Simulating a neutral system is always better.

No responsible scientist prefers charges perpetuated through the infinite
axises of the periodic box. Even if a nullifying correction usually
fixes it. ;)


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 773-570-0329              Fax:   217-244-6078
Salvatore Mario Cosseddu <> writes:
> Date: Thu, 27 Oct 2011 18:00:12 +0100
> From: Salvatore Mario Cosseddu <>
> To:
> Subject: namd-l:PME and net charge in the system
> User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-GB; rv:
>  Gecko/20110920 SUSE/3.1.15 Thunderbird/3.1.15
> Dear all,
> How NAMD manages a net charge in the system? i.e. A very big system
> with many charged elements where positive and negative charges are
> unbalanced, let's say total charge +3 or -4. My idea was that PME do
> not converge, But it seems that NAMD does not complain. May you tell
> me if some different approximations are used to handle these events?
> Regards
> Salvatore
> -- 
> Salvatore Cosseddu
> PhD student
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
> email:

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