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Monte Carlo Method for Calculating the Electrostatic Energy of a Molecule

Michael Mascagni6, 7 Contact Information and Nikolai A. Simonov7, 8 Contact Information

(6)  Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA
(7)  CSIT, Florida State University, Tallahassee, FL 32306, USA
(8)  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.

Contact Information Michael Mascagni
Email: mascagni@cs.fsu.edu

Contact Information Nikolai A. Simonov
Email: simonov@csit.fsu.edu
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