Ionic Charging Free Energies Using Ewald Summation
Recently, a number of groups have discovered that the use of Ewald summation leads to greatly improved stability in molecular dynamics simulations of nucleic acids, proteins and membrane bilayers. This presentation will discuss the effect of boundary conditions and treatment of long-range electrostatics on molecular dynamics simulations, as well as on the important problem of calculating free energy differences. Due to its simplicity, we focus on the problem of calculating ionic charging free energies. We review recent results that suggest Ewald summation gives appropriate values for this free energy, at least for the simple case of ion charging.
KeywordsFree Energy Molecular Dynamic Simulation Periodic Boundary Condition Radial Distribution Function Point Charge
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- S. Boresch and O. Steinhauser, Presumed versus real artifacts of the ewald summation technique: The importance of dielectric boundary conditions, Ber. Bunseges. Phys. Chem., 101:1019–1029, 1997.Google Scholar
- J. P. Valleau and S. G. Whittington, A guide to Monte Carlo for statistical mechanics: 1. Highways, In B. J. Berne, editor, Statistical Mechanics, Part A: Equilibrium Techniques, volume 5, New York, NY, 1977, Plenum.Google Scholar
- A. Toukmaji and J. A. Board, Ewald sum techniques in perspective: A survey, Comp. Phys. Comm., 95:78–92, 1996.Google Scholar
- S. Bogusz, T. Cheatham III, and B. Brooks, Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the ewald potential, J. Chem. Phys., 1998, 103:6177–6187 in press.Google Scholar