kth.sePublikationer
Ändra sökning
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions
Visa övriga samt affilieringar
2020 (Engelska)Ingår i: Supercomputing Frontiers and Innovations, ISSN 2409-6008, Vol. 7, nr 4, s. 62-67Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

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. 

Ort, förlag, år, upplaga, sidor
South Ural State University, Publishing Center , 2020. Vol. 7, nr 4, s. 62-67
Nyckelord [en]
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
Nationell ämneskategori
Datorteknik
Identifikatorer
URN: urn:nbn:se:kth:diva-302886DOI: 10.14529/jsfi200405Scopus ID: 2-s2.0-85101580336OAI: oai:DiVA.org:kth-302886DiVA, id: diva2:1599804
Anmärkning

QC 20211001

Tillgänglig från: 2021-10-01 Skapad: 2021-10-01 Senast uppdaterad: 2022-06-25Bibliografiskt granskad

Open Access i DiVA

Fulltext saknas i DiVA

Övriga länkar

Förlagets fulltextScopus

Person

Zhmurov, Artem

Sök vidare i DiVA

Av författaren/redaktören
Zhmurov, Artem
Av organisationen
Science for Life Laboratory, SciLifeLabParallelldatorcentrum, PDCSeRC - Swedish e-Science Research Centre
Datorteknik

Sök vidare utanför DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetricpoäng

doi
urn-nbn
Totalt: 19 träffar
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf