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GROMEX : A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation (2020)


Kohnke, B., Ullmann, T. R., Beckmann, A., Kabadshow, I., Haensel, D., Morgenstern, L., Dobrev, P., Groenhof, G., Kutzner, C., Hess, B., Dachsel, H., & Grubmüller, H. (2020). GROMEX : A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation. In H. Bungartz, S. Reiz, B. Uekermann, P. Neumann, & W. Nagel (Eds.), Software for Exascale Computing - SPPEXA 2016-2019 (pp. 517-543). Springer International Publishing. Lecture Notes in Computational Science and Engineering, 136. https://doi.org/10.1007/978-3-030-47956-5_17


JYU-tekijät tai -toimittajat


Julkaisun tiedot

Julkaisun kaikki tekijät tai toimittajatKohnke, Bartosz; Ullmann, Thomas R.; Beckmann, Andreas; Kabadshow, Ivo; Haensel, David; Morgenstern, Laura; Dobrev, Plamen; Groenhof, Gerrit; Kutzner, Carsten; Hess, Berk; et al.

EmojulkaisuSoftware for Exascale Computing - SPPEXA 2016-2019

Emojulkaisun toimittajatBungartz, H; Reiz, S; Uekermann, B; Neumann, P; Nagel, WE

ISBN978-3-030-47955-8

eISBN978-3-030-47956-5

Lehti tai sarjaLecture Notes in Computational Science and Engineering

ISSN1439-7358

eISSN2197-7100

Julkaisuvuosi2020

Sarjan numero136

Artikkelin sivunumerot517-543

KustantajaSpringer International Publishing

KustannuspaikkaCham

JulkaisumaaSveitsi

Julkaisun kielienglanti

DOIhttps://doi.org/10.1007/978-3-030-47956-5_17

Julkaisun avoin saatavuusAvoimesti saatavilla

Julkaisukanavan avoin saatavuusKokonaan avoin julkaisukanava

Julkaisu on rinnakkaistallennettu (JYX)https://jyx.jyu.fi/handle/123456789/73546


Tiivistelmä

Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an efficient and highly scalable way. Here we review and assess two of the main building blocks that will permit such simulations: (1) An electrostatics library based on the Fast Multipole Method (FMM) that treats local alternative charge distributions with minimal overhead, and (2) A $λ$-dynamics module working in tandem with the FMM that enables various types of chemical transitions during the simulation. Our $λ$-dynamics and FMM implementations do not rely on third-party libraries but are exclusively using C++ language features and they are tailored to the specific requirements of molecular dynamics simulation suites such as GROMACS. The FMM library supports fractional tree depths and allows for rigorous error control and automatic performance optimization at runtime. Near-optimal performance is achieved on various SIMD architectures and on GPUs using CUDA. For exascale systems, we expect our approach to outperform current implementations based on Particle Mesh Ewald (PME) electrostatics, because FMM avoids the communication bottlenecks caused by the parallel fast Fourier transformations needed for PME.


YSO-asiasanatbiomolekyylitsimulointisähköstatiikka


Liittyvät organisaatiot

JYU-yksiköt:


OKM-raportointiKyllä

Raportointivuosi2020

JUFO-taso1


Viimeisin päivitys 2024-26-03 klo 09:18