[gmx-users] Charge correction PME

[David van der Spoel]

On 2013-11-30 18:01, Mark Abraham wrote:
> ... but not necessarily any good! See
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html.
> I have seen Gerrit present some convincing results since then, but they do
> not seem to be in press, yet.
>
> Neutralizing explicitly seems like the right course just about always!
>
> I'm never sure why people think extracting an energy component means
> anything; extracting part of an intrinsically global one seems even less
> likely to mean anything... Do enlighten me! :-)

I think you are formulating this somehow too general. Enthalpy and 
entropy are energy components, but interaction energies can yield 
insights as well. However looking at Coulomb and Van der Waals energies 
separately does not make sense as these terms are fitted together to 
reproduce total energies. As regards the former kind of energy 
decomposition I can recommend my recent papers e.g.: (this also explain 
why you should never use implicit solvent):

Haiyang Zhang, Tianwei Tan, Csaba Hetényi and David van der Spoel: 
Quantification of solvent contribution to the stability of non-covalent 
complexes J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013) 
http://pubs.acs.org/doi/abs/10.1021/ct400404q

>
> Mark
>
>
> On Sat, Nov 30, 2013 at 5:29 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
>
>> I might be wrong here, but my expectation is that nowadays you should
>> not do anything explicitly in this regard. The compensating charge is
>> automatically applied.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila
>> <benrezkallah at gmail.com> wrote:
>>> Dear gmx_users,
>>>   My question is about the coulomb LR contribution with PME, I can't
>> access
>>> to david's original post treating this subject in the mailing list (
>>> http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html) if it
>>> exists, because some links are disabled.If any one can send me the page?
>>> I'm working on a protein in explicit solvent (water) at different
>>> concentration of salt (NaCl).I need to calculate coulomb LR energy
>>> interaction between some residues and Cl-/Na+.
>>>   My question is :should I turn off the charge correction ( when
>> calculating
>>> electrostatics for no neutral system),and how to do it? or it has a small
>>> contribution to the energy, and I have no worry about it.
>>>
>>> I hope find answers in your replies.
>>>
>>> respectively,
>>> Djamila Benrezkallah
>>> University of Oran
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se