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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...

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Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
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.
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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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