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

eric jakobsson jake at ncsa.uiuc.edu
Sun Oct 10 20:27:41 CEST 2004

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.


At 02:20 PM 10/10/2004, you wrote:
>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 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
>gmx-users mailing list
>gmx-users at gromacs.org
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Eric Jakobsson, Ph.D.
Professor, Molecular and Integrative Physiology, Biophysics and 
Computational Biology, Beckman Institute, Bioengineering, Biochemistry, and 
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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