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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware type...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549999/ https://www.ncbi.nlm.nih.gov/pubmed/28746339 http://dx.doi.org/10.1371/journal.pcbi.1005659 |
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author | Eastman, Peter Swails, Jason Chodera, John D. McGibbon, Robert T. Zhao, Yutong Beauchamp, Kyle A. Wang, Lee-Ping Simmonett, Andrew C. Harrigan, Matthew P. Stern, Chaya D. Wiewiora, Rafal P. Brooks, Bernard R. Pande, Vijay S. |
author_facet | Eastman, Peter Swails, Jason Chodera, John D. McGibbon, Robert T. Zhao, Yutong Beauchamp, Kyle A. Wang, Lee-Ping Simmonett, Andrew C. Harrigan, Matthew P. Stern, Chaya D. Wiewiora, Rafal P. Brooks, Bernard R. Pande, Vijay S. |
author_sort | Eastman, Peter |
collection | PubMed |
description | OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community. |
format | Online Article Text |
id | pubmed-5549999 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-55499992017-08-15 OpenMM 7: Rapid development of high performance algorithms for molecular dynamics Eastman, Peter Swails, Jason Chodera, John D. McGibbon, Robert T. Zhao, Yutong Beauchamp, Kyle A. Wang, Lee-Ping Simmonett, Andrew C. Harrigan, Matthew P. Stern, Chaya D. Wiewiora, Rafal P. Brooks, Bernard R. Pande, Vijay S. PLoS Comput Biol Research Article OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community. Public Library of Science 2017-07-26 /pmc/articles/PMC5549999/ /pubmed/28746339 http://dx.doi.org/10.1371/journal.pcbi.1005659 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Eastman, Peter Swails, Jason Chodera, John D. McGibbon, Robert T. Zhao, Yutong Beauchamp, Kyle A. Wang, Lee-Ping Simmonett, Andrew C. Harrigan, Matthew P. Stern, Chaya D. Wiewiora, Rafal P. Brooks, Bernard R. Pande, Vijay S. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title_full | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title_fullStr | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title_full_unstemmed | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title_short | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics |
title_sort | openmm 7: rapid development of high performance algorithms for molecular dynamics |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549999/ https://www.ncbi.nlm.nih.gov/pubmed/28746339 http://dx.doi.org/10.1371/journal.pcbi.1005659 |
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