Abstract
A linear (elliptic) problem in molecular electrostatics is considered. To solve it, we propose an efficient Monte Carlo algorithm. The method utilizes parallel computing of point potential values. It is based on the walk-in-subdomains technique, walk-on-spheres algorithm, and an exact treatment of boundary conditions.
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Mascagni, M., Simonov, N.A.: Monte Carlo method for calculating the electrostatic energy of a molecule. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J., Zomaya, A.Y. (eds.) ICCS 2003. LNCS, vol. 2657, pp. 63–74. Springer, Heidelberg (2003)
Mascagni, M., Simonov, N.A.: Monte Carlo methods for calculating some physical properties of large molecules. SIAM Journal on Scientific Computing 26, 339–357 (2004)
Davis, M.E., McCammon, J.A.: Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90, 509–521 (1990)
Simonov, N.A.: A random walk algorithm for the solution of boundary value problems with partition into subdomains. In: Metody i algoritmy statisticheskogo modelirovanija, Akad. Nauk SSSR Sibirsk. Otdel., Vychisl. Tsentr, Novosibirsk, pp. 48–58 (1983)
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Fleming, C., Mascagni, M., Simonov, N. (2005). An Efficient Monte Carlo Approach for Solving Linear Problems in Biomolecular Electrostatics. In: Sunderam, V.S., van Albada, G.D., Sloot, P.M.A., Dongarra, J. (eds) Computational Science – ICCS 2005. ICCS 2005. Lecture Notes in Computer Science, vol 3516. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11428862_103
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DOI: https://doi.org/10.1007/11428862_103
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