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

Ran Friedman ran at hemi.tau.ac.il
Sun Oct 10 21:20:18 CEST 2004


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

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