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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...

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Autores principales: Maeda, Satoshi, Harabuchi, Yu, Takagi, Makito, Saita, Kenichiro, Suzuki, Kimichi, Ichino, Tomoya, Sumiya, Yosuke, Sugiyama, Kanami, Ono, Yuriko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
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.
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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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