[gmx-developers] Simulation of net-charged systems in gmx
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Mon Nov 12 12:06:17 CET 2012
thanks for the useful comments. I have checked the paper again and it
tuns out that they did test the correction also on a inhomogeneous system:
/To////further illustrate the effects of charge on the Ewald method//
//we have performed similar calculations on two other systems//
//in vacuo: a deprotonated acetate molecule and sperm whale//
//myoglobin protein. Calculations of the electrostatics both//
//with and without the net-charge correction on this protein//
//system tests the validity of correcting the net-charge interactions//
//with a simple point charge calculation on a system//
//much more complex than the three-ion system./
Since the proposed correction seems to be implemented only in CHARMM
version 25 and refined in version 26, and not in Gromacs, it's not
relevant for me from a pragmatical point of view.
On 11/08/2012 12:11 PM, Gerrit Groenhof wrote:
> 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.
>> > 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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| Luis Felipe Pineda De Castro, PhD |
| Computational Chemist - Postdoc |
| Computational Chemistry and |
| Biochemistry Laboratory |
| School of Natural Sciences |
| Linnaeus University |
| SE-391 82 Kalmar |
| Norrgård, room 311 |
| Sweden - Sverige |
| Phone: ++46-480-44 6329 |
| Mobile: ++46-76-8420572 |
| E-Mail: luis.pinedadecastro at lnu.se|
| Web: lnu.se |
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