Long-range electrostatic effects in biomolecular simulations

The appropriate treatment of long-range Coulombic forces is an area of great interest in the biomolecular simulation community. Recently a number of fast algorithms for handling the so-called N-body problem have appeared. In particular, methods for efficient calcule of Ewald sums are of great interest. In addition, theoretical questions relating to the marriage of periodic boundary conditions with Coulombic interactions are still of interest. In this paper, we first discuss some issues relating to the use of Ewald summation, and then discuss fast algorithms for its calculation. We focus on algorithms based on the Particle-Mesh approach. In particular we compare the P3M algorithm implemented by Pollock and Glosli [1] with the PME algorithms developed by our group, and report on a new “optimized” PME algorithm.