A Hybrid Explicit/Implicit Solvent Technique for Biomolecular Simulations
Final rept. Oct 2002-Aug 2003
ARMY RESEARCH LAB ABERDEEN PROVING GROUND MD COMPUTATIONAL AND INFORMATION SCIENCES
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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.
- Physical Chemistry
- Numerical Mathematics
- Electricity and Magnetism