[gmx-users] Long range interaction energy of charged particles with PME - GMX 3.3.1

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 1 19:50:33 CEST 2006

> I was not accurate. E(LR) is the total PME energy, and the rest can be 
> extracted by neutralising selected groups. So the binding energy can 
> calculated from: E(LR)-E(sol-sol)- E(ligand-ligand)- 
> E(protein-protein)-E(solvent-ligand)-E(solvent-protein), where e.g. 
> E(sol-sol) can be calculated when the protein and the ligand are both 
> made uncharged. This still leaves us with the PME correction.
> I think that deltaG calculations with charged particles and periodic 
> systems are much more difficult than the interaction energy, and I do 
> not deal with them.
Just for your information, Erik and I are writing this up in the context 
of free energy calculations. We could probably upload a draft to arXiv.
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://folding.bmc.uu.se

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