New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the per...

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Bibliographic Details
Published in:	Journal of computational chemistry Vol. 42; no. 4; pp. 231 - 241
Main Authors:	Jung, Jaewoon, Kobayashi, Chigusa, Kasahara, Kento, Tan, Cheng, Kuroda, Akiyoshi, Minami, Kazuo, Ishiduki, Shigeru, Nishiki, Tatsuo, Inoue, Hikaru, Ishikawa, Yutaka, Feig, Michael, Sugita, Yuji
Format:	Journal Article
Language:	English
Published:	Hoboken, USA John Wiley & Sons, Inc 05.02.2021 Wiley Subscription Services, Inc
Subjects:	Algorithms ARM CPU architecture Central processing units Computational Biology - methods CPUs DNA - chemistry fast Fourier transform Fugaku supercomputer Molecular dynamics Molecular Dynamics Simulation parallel input/output setup RNA - chemistry Simulation ARM CPU architecture parallel input/output setup fast Fourier transform Fugaku supercomputer molecular dynamics simulation
ISSN:	0192-8651, 1096-987X, 1096-987X
Online Access:	Get full text
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