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  GROMEX: A scalable and versatile fast multipole method for biomolecular simulation

Kohnke, B., Ullmann, R. T., Beckman, A., Kabadshow, I., Haensel, D., Morgenstern, L., et al. (2020). GROMEX: A scalable and versatile fast multipole method for biomolecular simulation. In H.-J. Bungartz, S. Reiz, B. Uekermann, P. Neumann, & W. E. Nagel (Eds.), Software for Exascale Computing - SPPEXA 2016-2019 (pp. 517-543). Cham: Springer. doi:10.1007/978-3-030-47956-5_17.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-D91C-7 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-175B-A
Genre: Book Chapter

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 Creators:
Kohnke, B.1, Author              
Ullmann, R. T.1, Author              
Beckman, A., Author
Kabadshow, I., Author
Haensel, D., Author
Morgenstern, L., Author
Dobrev, P.2, Author              
Groenhof, G.2, Author              
Kutzner, C.2, Author              
Hess, B., Author
Dachsel, H., Author
Grubmüller, H.2, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society, ou_578631              
2Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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Free keywords: open access; computational algorithms and numerical methods; data management and exploration; high-performance computing; simulation software and applications; system software and software tools
 Abstract: Atomistic simulations of large biomolecular systems with chemicalvariability such as constant pH dynamic protonation offer multiple challenges inhigh performance computing. One of them is the correct treatment of the involvedelectrostatics in an efficient and highly scalable way. Here we review and assess twoof the main building blocks that will permit such simulations: (1) An electrostaticslibrary based on the Fast Multipole Method (FMM) that treats local alternativecharge distributions with minimal overhead, and (2) Aλ-dynamics module workingin tandem with the FMM that enables various types of chemical transitions duringthe simulation. Ourλ-dynamics and FMM implementations do not rely on third-party libraries but are exclusively using C++ language features and they aretailored to the specific requirements of molecular dynamics simulation suites suchas GROMACS. The FMM library supports fractional tree depths and allows forrigorous error control and automatic performance optimization at runtime. Near-optimal performance is achieved on various SIMD architectures and on GPUsusing CUDA. For exascale systems, we expect our approach to outperform currentimplementations based on Particle MeshEwald (PME) electrostatics, becauseFMM avoids the communication bottlenecks caused by the parallel fast Fouriertransformations needed for PME.

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Language(s): eng - English
 Dates: 2020-07-312020
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1007/978-3-030-47956-5_17
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Title: Software for Exascale Computing - SPPEXA 2016-2019
Source Genre: Proceedings
 Creator(s):
Bungartz, H.-J., Editor
Reiz, S., Editor
Uekermann, B., Editor
Neumann, P., Editor
Nagel, W. E., Editor
Affiliations:
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Publ. Info: Cham : Springer
Pages: XI, 610 Volume / Issue: - Sequence Number: - Start / End Page: 517 - 543 Identifier: ISBN: 978-3-030-47955-8

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Title: Lecture Notes in Computational Science and Engineering
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Pages: - Volume / Issue: 136 Sequence Number: - Start / End Page: - Identifier: -