[gmx-developers] Simulation of net-charged systems in gmx
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Mon Nov 12 13:08:07 CET 2012
Hi!
thanks for commenting. The authors address both the pressure and the
free-energy artifacts due to the neutralizing plasma/background charge
in PME simulations. So the pressure artifact was also considered in the
protein example, and the proposed correction was able to significantly
decrease both.
In the meantime I am aware of the artifacts you mention and I assume you
are right and better suited than me to assess the advantages of such a
correction. I only would like to simulate a charged, hydrated membrane
system if there is no objections against that from a theoretical point
of view (to find this out was the original goal of these postings), and
if there is a corresponding implementation in Gromacs, what is not the
case. Therefore I will add counter ions or otherwise neutralize the
system, as usual. Nevertheless, it would be nice to have an ion-free
reference state to compare with systems containing salt and so better
assess the effect of the ions.
Best,
Felipe
On 11/12/2012 12:46 PM, Gerrit Groenhof wrote:
> Hi,
>
> But they did not look at the free energy profile of an ion moving
> across the system, only total electrostatic energy in these two cases.
>
> In a true non-homegenous system, such as lipid bilayer in water, you
> will see artefacts if the system is non-neutral, with the free energy
> of the ion inside the lower dielectric either too high or too low,
> depending on the signs and magnitudes of the ion and net charge in the
> system. We have not tried, but I don't see how the correction would
> alleviate that problem. In their scheme, the correction term would be
> independent of the position of the test particle.
>
> It is not clear to me why you want to simulate a net charged system.
> Can't you avoid this by adding counterions?
>
> Gerrit
>
>
>
>
> On Nov 12, 2012, at 1:06 PM, Felipe Pineda, PhD wrote:
>
>> Hi,
>>
>> 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.
>>
>> Kind regards,
>>
>> Felipe
>>
>> On 11/08/2012 12:11 PM, Gerrit Groenhof wrote:
>>> Hi,
>>>
>>> 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.
>>>
>>> Best,
>>>
>>> Gerrit
>>>
>>>
>>>
>>>
>>>> -------- 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.
>>>>
>>>> -Justin
>>>>
>>>> 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
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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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 <http://lnu.se> |
>> +-----------------------------------+
>
--
+-----------------------------------+
| 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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