FAST SUMMATION BOUNDARY-ELEMENT METHOD FOR CALCULATING SOLVATION FREE-ENERGIES OF MACROMOLECULES

We present a boundary element method (BEM) for calculating the reactio n field energy of a macromolecule embedded in a high-dielectric medium such as water. In a BEM calculation, the key computational task is th e calculation of the induced surface charge distribution at the dielec tric boundary. This is obtained by solving a system of linear equation s whose dimension can run into the tens of thousands for a macromolecu le. In this work, we use a fast summation hierarchical multipole metho d to solve for the induced surface charge densities. By careful analys is of the levels of approximation required for the various terms in th e calculation, we avoid the unnecessary computation of terms that cont ribute negligibly to the final outcome and, consequently, achieve high computational efficiency. For a protein such as BPTI with 890 atoms, the calculation of the induced surface charge density distribution and the reaction field energy was completed in 7.9 s on an SGI workstatio n with an R10000 CPU. (C) 1998 John Wiley & Sons, Inc. J Comput Chem 1 9: 1494-1504, 1998.