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
GROMACS 4.0: Algorithms for highly efficient, load balanced, and scalable molecular simulation
Max-Planck Institut Mainz.ORCID-id: 0000-0002-7498-7763
Max-Planck Institut Göttingen.
Uppsala University.
Stockholm University.ORCID-id: 0000-0002-2734-2794
2008 (Engelska)Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, nr 2, s. 435-Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs; for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

Ort, förlag, år, upplaga, sidor
2008. Vol. 4, nr 2, s. 435-
Nationell ämneskategori
Teoretisk kemi Biofysik
Identifikatorer
URN: urn:nbn:se:kth:diva-82695DOI: 10.1021/ct700301qISI: 000254277900007Scopus ID: 2-s2.0-46249092554OAI: oai:DiVA.org:kth-82695DiVA, id: diva2:498520
Anmärkning
QC 20120217Tillgänglig från: 2012-02-12 Skapad: 2012-02-12 Senast uppdaterad: 2020-05-11Bibliografiskt granskad

Open Access i DiVA

Fulltext saknas i DiVA

Övriga länkar

Förlagets fulltextScopus

Personposter BETA

Hess, BerkLindahl, Erik

Sök vidare i DiVA

Av författaren/redaktören
Hess, BerkLindahl, Erik
I samma tidskrift
Journal of Chemical Theory and Computation
Teoretisk kemiBiofysik

Sök vidare utanför DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetricpoäng

doi
urn-nbn
Totalt: 68 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