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New ways to boost molecular dynamics simulations
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680170/ https://www.ncbi.nlm.nih.gov/pubmed/25824339 http://dx.doi.org/10.1002/jcc.23899 |
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author | Krieger, Elmar Vriend, Gert |
author_facet | Krieger, Elmar Vriend, Gert |
author_sort | Krieger, Elmar |
collection | PubMed |
description | We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time‐step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a “densostat,” and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. |
format | Online Article Text |
id | pubmed-6680170 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-66801702019-08-09 New ways to boost molecular dynamics simulations Krieger, Elmar Vriend, Gert J Comput Chem Full Papers We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time‐step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a “densostat,” and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. John Wiley and Sons Inc. 2015-03-30 2015-05-15 /pmc/articles/PMC6680170/ /pubmed/25824339 http://dx.doi.org/10.1002/jcc.23899 Text en © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Full Papers Krieger, Elmar Vriend, Gert New ways to boost molecular dynamics simulations |
title | New ways to boost molecular dynamics simulations |
title_full | New ways to boost molecular dynamics simulations |
title_fullStr | New ways to boost molecular dynamics simulations |
title_full_unstemmed | New ways to boost molecular dynamics simulations |
title_short | New ways to boost molecular dynamics simulations |
title_sort | new ways to boost molecular dynamics simulations |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680170/ https://www.ncbi.nlm.nih.gov/pubmed/25824339 http://dx.doi.org/10.1002/jcc.23899 |
work_keys_str_mv | AT kriegerelmar newwaystoboostmoleculardynamicssimulations AT vriendgert newwaystoboostmoleculardynamicssimulations |