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Implementation and performance of the artificial force induced reaction method in the GRRM17 program
This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pullin...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765425/ https://www.ncbi.nlm.nih.gov/pubmed/29135034 http://dx.doi.org/10.1002/jcc.25106 |
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author | Maeda, Satoshi Harabuchi, Yu Takagi, Makito Saita, Kenichiro Suzuki, Kimichi Ichino, Tomoya Sumiya, Yosuke Sugiyama, Kanami Ono, Yuriko |
author_facet | Maeda, Satoshi Harabuchi, Yu Takagi, Makito Saita, Kenichiro Suzuki, Kimichi Ichino, Tomoya Sumiya, Yosuke Sugiyama, Kanami Ono, Yuriko |
author_sort | Maeda, Satoshi |
collection | PubMed |
description | This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. |
format | Online Article Text |
id | pubmed-5765425 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-57654252018-02-01 Implementation and performance of the artificial force induced reaction method in the GRRM17 program Maeda, Satoshi Harabuchi, Yu Takagi, Makito Saita, Kenichiro Suzuki, Kimichi Ichino, Tomoya Sumiya, Yosuke Sugiyama, Kanami Ono, Yuriko J Comput Chem Software News and Updates This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. John Wiley and Sons Inc. 2017-11-14 2018-02-05 /pmc/articles/PMC5765425/ /pubmed/29135034 http://dx.doi.org/10.1002/jcc.25106 Text en © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs (http://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. |
spellingShingle | Software News and Updates Maeda, Satoshi Harabuchi, Yu Takagi, Makito Saita, Kenichiro Suzuki, Kimichi Ichino, Tomoya Sumiya, Yosuke Sugiyama, Kanami Ono, Yuriko Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title | Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title_full | Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title_fullStr | Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title_full_unstemmed | Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title_short | Implementation and performance of the artificial force induced reaction method in the GRRM17 program |
title_sort | implementation and performance of the artificial force induced reaction method in the grrm17 program |
topic | Software News and Updates |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765425/ https://www.ncbi.nlm.nih.gov/pubmed/29135034 http://dx.doi.org/10.1002/jcc.25106 |
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