Periodic Coulomb Tree Method: An Alternative to Parallel Particle Mesh Ewald

Henry A Boateng

doi:10.1021/acs.jctc.9b00648

Periodic Coulomb Tree Method: An Alternative to Parallel Particle Mesh Ewald

J Chem Theory Comput. 2020 Jan 14;16(1):7-17. doi: 10.1021/acs.jctc.9b00648. Epub 2019 Dec 9.

Author

Henry A Boateng^{1

2}

Affiliations

¹ Department of Mathematics , San Francisco State University , 1600 Holloway Ave. , San Francisco , California 94132 , United States.
² Department of Mathematics , Bates College , 2 Andrews Rd. , Lewiston , Maine 04240 , United States.

PMID: 31747267
DOI: 10.1021/acs.jctc.9b00648

Abstract

Particle mesh Ewald (PME) is generally the method of choice for handling electrostatics in simulations with periodic boundary conditions. The excellent efficiency of PME on low processor counts is largely due to the use of the fast Fourier transform (FFT). However, due to the FFT's high communication cost, PME scales poorly in parallel. We develop a periodic Coulomb tree (PCT) method for electrostatic interactions in periodic boundary conditions as an alternative to PME in parallel simulations. We verify the accuracy of PCT by comparison of structural and dynamical properties of three different systems obtained via MD simulations using PME and PCT and provide parallel timing comparisons of the two methods on up to 1024 cores.