Keyrouz, W.
, Hamlin, P.
, Thrasher, W.
and Mascagni, M.
(2019),
Geometry Entrapment in Walk-on-Subdomains, Monte Carlo Methods and Applications, [online], https://doi.org/10.1515/mcma-2019-2052, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=928248
(Accessed April 19, 2024)
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Geometry Entrapment in Walk-on-Subdomains
Published
Author(s)
, Preston Hamlin, W. J. Thrasher,
Abstract
One method of computing the electrostatic energy of a biomolecule in a solution combines the Walk-On-Spheres and Walk-On-Subdomains Monte Carlo algorithms. In the course of examining an implementation of this method, a performance issue was discovered in the Walk-On-Subdomains portion of the algorithm. The problem occurs when a walker repeatedly oscillates between two subdomains and is trapped eventually in a small area, which causes a large increase in runtime. This issue is described in detail and a potential solution is examined.Citation
Monte Carlo Methods and Applications
Volume
25
Issue
4
Pub Type
Journals
Download Paper
Keywords
Monte Carlo, Walk on Subdomains, Brownian Motion, Poisson-Boltzmann, Walk Entrapment
Citation
Created November 18, 2019, Updated October 12, 2021