A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules

Abstract

At present, there are two widely used approaches for computing molecular hydration and electrostatic effects within the continuum approximation: the finite difference method, in which the electric potential is directly computed on a cubic grid, and the induced polarization charge or boundary element method, in which an induced charge distribution is first computed on the molecular surface and in which solvation effects are then calculated by reference to the reaction field arising from this induced surface charge. While the induced surface charge approach has a number of advantages over finite differences, especially in the computation of hydration forces and solvent stabilization, the applications of this technique have been largely restricted to small molecules. This is primarily due to the very large system of equations that results when the surface of a macromolecule is discretized into elements small enough to ensure an acceptable level of numerical accuracy within the continuum model. This article describes a new algorithm for implementing boundary element calculations within the continuum model. The essence of our approach is only to compute explicitly those interactions between surface elements that are relatively close together and to approximate long-range interactions by grid-based multipole expansion. The resulting system of equations has a relatively sparse coefficient matrix and requires disk storage that increases linearly with molecular surface area. The technique has numerous applications in the analysis of solvation effects in large molecules, especially in the area of conformational analysis, where it is critical to accurately estimate the global hydration energy for the entire structure. © 1996 by John Wiley & Sons, Inc.