onr:"swepub:oai:DiVA.org:kth-302886"
Search: onr:"swepub:oai:DiVA.org:kth-302886" > Update on Performan...
- 1 of 1
- Previous record
- Next record
- To hitlist
Update on Performance Analysis of Different Computational Architectures : Molecular Dynamics in Application to Protein-Protein Interactions
- Fedorov, V. A. (author)
- Kholina, E. G. (author)
- Kovalenko, I. B. (author)
- show more...
- Gudimchuk, N. B. (author)
- Orekhov, P. S. (author)
- show less...
- (creator_code:org_t)
- South Ural State University, Publishing Center, 2020
- 2020
- English.
- In: Supercomputing Frontiers and Innovations. - : South Ural State University, Publishing Center. - 2409-6008 .- 2313-8734. ; 7:4, s. 62-67
- Journal article (peer-reviewed)
Abstract
Subject headings
Close
- Molecular dynamics has proved itself as a powerful computer simulation method to study dynamics, conformational changes, and interactions of biological macromolecules and their complexes. In order to achieve the best performance and efficiency, it is crucial to benchmark various hardware platforms for the simulations of realistic biomolecular systems with different size and timescale. Here, we compare performance and scalability of a number of commercially available computing architectures using all-atom and coarse-grained molecular dynamics simulations of water and the Ndc80-microtubule protein complex in the GROMACS-2019.4 package. We report typical single-node performance of various combinations of modern CPUs and GPUs, as well as multiple-node performance of the “Lomonosov-2” supercomputer. These data can be used as the practical guidelines for choosing optimal hardware for molecular dynamics simulations.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datorteknik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Engineering (hsv//eng)
Keyword
- coarse grain
- microtubule
- molecular dynamics
- Ndc80
- tubulin
- Benchmarking
- Bioinformatics
- Computational chemistry
- Computer hardware
- Program processors
- Proteins
- Supercomputers
- Biological macromolecule
- Coarse-grained molecular dynamics simulations
- Computational architecture
- Computing architecture
- Molecular dynamics simulations
- Performance and scalabilities
- Protein-protein interactions
- Single-node performance
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
- Supercomputing Frontiers and Innovations (Search for host publication in LIBRIS)
To the university's database
- 1 of 1
- Previous record
- Next record
- To hitlist
Find more in SwePub
- By the author/editor
- Fedorov, V. A.
- Kholina, E. G.
- Kovalenko, I. B.
- Gudimchuk, N. B.
- Orekhov, P. S.
- Zhmurov, Artem
- About the subject
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Computer and Inf ...
- and Computer Enginee ...
- Articles in the publication
- Supercomputing F ...
- By the university
- Royal Institute of Technology
Search outside SwePub
- Extend your search to:
- Google Book Search
- Google Scholar
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
- Copyright © LIBRIS - National Library Systems
- LIBRIS.kb.se
