[gmx-developers] Simulation of net-charged systems in gmx
ggroenh at gwdg.de
Thu Nov 8 12:11:22 CET 2012
The net-charge correction by B. Brooks and co-workers corrects for total energy and pressure artefacts only in homogeneous systems as far as I understand it.
However, there are serious artefacts on the free energy profiles (and thus partitioning) of charged particles in boxes with inhomogeneous dielectric media (such as proteins, lipid bilayers, and almost everything else that is biologically relevant). These artefacts cannot be corrected by the aforementioned approach. Only explicit neutralization by means of counter ions can lead to meaningful results.
> -------- 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.
> > <http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1>).
> > 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?
> >> http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html
> >> 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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