[gmx-developers] Simulation of net-charged systems in gmx

Felipe Pineda, PhD luis.pinedadecastro at lnu.se
Thu Nov 8 08:58:17 CET 2012

-------- Original Message --------
Subject: 	Re: [gmx-users] Simulation of charged systems (2)
Date: 	Tue, 6 Nov 2012 18:21:57 +0100
From: 	Justin Lemkul <jalemkul at vt.edu>
To: 	Luis Felipe Pineda de Castro <luis.pinedadecastro at lnu.se>

(Replied off-list)

I think it would be more productive to post this to gmx-developers rather than
gmx-users, since it really is an inquiry about the code itself.  The core
developers usually don't reply to gmx-users, and they're the ones who will have
the answers.  My inclination is that the answer to your question (now that it's
more clear what you're asking) is "no," but since I have no direct knowledge of
the PME code, I can't say for certain.


On 11/6/12 3:27 AM, Felipe Pineda, PhD wrote:
> Hi,
> thanks to Justin for the pointer to the list archive I searched before with "net
> charge", but without getting useful results. For the sake of clarity, I am not
> referring to the "neutralizing plasma" or neutralizing background charge used
> implicitly with PME, but to an additional net-charge correction implemented for
> example in CHARMM to avoid, at least partly, the artifacts produced by that
> neutralizing background charge in net-charged systems, which are sometimes
> unavoidable (s., eg., Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and
> free energy artifacts in charged periodic systems via net charge corrections to
> the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84.
> Felipe
> On 11/05/2012 02:27 PM, Justin Lemkul wrote:
>> On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote:
>>> Hi again!
>>> many thanks to Xavier for his response, the only one I got so far ... I had the
>>> same impression, but I'm seeking for theoretically/technically more funded
>>> statements. My impression is also that there are different kind of "equations"
>>> depending of the treatment of long-range electrostatic interactions.
>>> My concrete question is now: are net charge corrections to the Ewald potential
>>> implemented in Gromacs?
>> Searching the list archive for "neutralizing background charge" turns up a large
>> number of results.  This is a fairly common question, and there are many replies
>> with varying degrees of detail.
>> -Justin


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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