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

[David van der Spoel]

On Mon, 2004-10-11 at 15:39, Ran Friedman wrote:
> 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?
> 
This isn't taken into consideration anywhere so you'll have to check the
correction to the energy that is used for charged systems.
I'm not sure whether it is in the manual.
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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