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Monte Carlo Method for Calculating the Electrostatic Energy of a Molecule
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Monte Carlo Method for Calculating the Electrostatic Energy of a Molecule
Michael Mascagni6, 7 and Nikolai A. Simonov7, 8 
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Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA |
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CSIT, Florida State University, Tallahassee, FL 32306, USA |
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ICM&MG, Lavrentjeva 6, Novosibirsk, 630090, Russia |
Abstract
The problem of computing the electrostatic energy of a large molecule is considered. It is reduced to solving the Poisson
equation inside and the linear Poisson-Boltzmann equation in the exterior, coupled by boundary conditions. A Monte Carlo estimate
for the potential point values, their derivatives, and the energy is constructed. The estimate is based on the walk on spheres
and Green’s function first passage algorithms; the walk in subdomains technique; and finite-difference approximations of the
boundary condition. Results of some illustrative calculations are presented.
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