[gmx-users] Interaction energy of charged particles with PME

[Ran Friedman]

I'm afraid I wasn't clear enough. What you describe is the usual thing 
to do when one simulates a charged system. However, when you want to 
calculate the long range Coulomb term between e.g. your protein and a 
ligand, you have to recalculate the long range Coulomb term after 
neutralising the charge of the protein (and repeat the same procedure 
for the ligand) using mdrun -rerun in Gromacs. In that case, the system 
in the example given below will carry a net charge of +5. My problem, 
therefore, is how to calculate the interaction energies in those cases?

eric jakobsson wrote:

> To make the whole system neutral, we generally use unequal numbers of 
> positive and negative ions in the electrolyte environment of the 
> system.  For example, if a protein is carrying a net charge of -5, we 
> might have 40 potassium ions and 35 chloride ions in the electrolyte.  
> That is the atomically explicit correspondence to Debye-Huckel 
> screening, which states that the vicinity of charged macromolecules 
> will attract an excess of oppositely charged electrolyte ions, with 
> net electroneutrality within a volume that includes electrolyte out to 
> a Debye length away from the protein surface, about 10 angstroms in 
> physiological salt concentration.
>
> Eric
>
> At 02:20 PM 10/10/2004, you wrote:
>
>> Hi,
>>
>> The topic of the calculation of interaction energies with PME was 
>> raised before, but I still have a problem following David van der 
>> Spoel's message at 
>> http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html
>>
>> My problem is as follows: I want to calculate the interaction 
>> energies between a charged protein and a charged ligand. If I make 
>> either of them neutral, the whole system will be charged. Will the 
>> energies I get make sense anyway? How can I correct or account for that?
>>
>> Your help will be appreciated,
>> Ran.
>>
>> -- 
>> ------------------------------------------------------
>> Ran Friedman
>> Laser Laboratory for Fast Reactions in Biology
>> Department of Biochemistry
>> Faculty of Life Sciences
>> Tel-Aviv University
>> Tel. +972-3-6409824
>> Fax. +972-3-6409875
>> ------------------------------------------------------
>>
>>
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>
>
> Eric Jakobsson, Ph.D.
> Professor, Molecular and Integrative Physiology, Biophysics and 
> Computational Biology, Beckman Institute, Bioengineering, 
> Biochemistry, and Neuroscience.
> Senior Research Scientist, National Center for Supercomputing 
> Applications
> 4021 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Avenue
> Urbana, IL 61801
> ph 217-244-2896
> fax 217-244-2909
> e-mail jake at ncsa.uiuc.edu
>
> (Since May 2003 I have been on leave from the University of Illinois 
> to serve as the Chair of the NIH Biomedical Information Science and 
> Technology Consortium and the NIGMS Center for Bioinformatics and 
> Computational Biology, in Bethesda, Maryland.  However I commute to 
> Urbana almost every week to maintain my research lab here.
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-- 
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------