A3 Kirjan tai muun kokoomateoksen osa
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 toimittajat: Kohnke, Bartosz; Ullmann, Thomas R.; Beckmann, Andreas; Kabadshow, Ivo; Haensel, David; Morgenstern, Laura; Dobrev, Plamen; Groenhof, Gerrit; Kutzner, Carsten; Hess, Berk; et al.

Emojulkaisu: Software for Exascale Computing - SPPEXA 2016-2019

Emojulkaisun toimittajat: Bungartz, H; Reiz, S; Uekermann, B; Neumann, P; Nagel, WE

ISBN: 978-3-030-47955-8

eISBN: 978-3-030-47956-5

Lehti tai sarja: Lecture Notes in Computational Science and Engineering

ISSN: 1439-7358

eISSN: 2197-7100

Julkaisuvuosi: 2020

Sarjan numero: 136

Artikkelin sivunumerot: 517-543

Kustantaja: Springer International Publishing

Kustannuspaikka: Cham

Julkaisumaa: Sveitsi

Julkaisun kieli: englanti

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

Julkaisun avoin saatavuus: Avoimesti saatavilla

Julkaisukanavan avoin saatavuus: Kokonaan 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-asiasanat: biomolekyylit; simulointi; sähköstatiikka

Liittyvät organisaatiot

OKM-raportointi: Kyllä

VIRTA-lähetysvuosi: 2020

JUFO-taso: 1