A Hybrid/Explicit/Implicit Solvent Technique for Biomolecular Simulations

Report No. ARL-TR-3268
Authors: Michael S. Lee and Mark A. Olson
Date/Pages: August 2004; 24 pages
Abstract: In this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
Distribution: Approved for public release
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Last Update / Reviewed: August 1, 2004