Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states

An algorithm to locate transition states on a potential energy surface (PES) is proposed and described. The technique is based on the GAD method where the gradient of the PES is projected into a given direction and also perpendicular to it. In the proposed method, named GAD-CD, the projection is not...

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Autores: Bofill i Villà, Josep M., Ribas Ariño, Jordi, Valero Montero, Rosendo, Albareda, Guillermo, Moreira, Ibério de Pinho Ribeiro, Quapp, Wolfgang
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2019
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/152811
Acceso en línea:https://hdl.handle.net/2445/152811
Access Level:acceso abierto
Palabra clave:Dinàmica molecular
Algorismes computacionals
Química física
Molecular dynamics
Computer algorithms
Physical and theoretical chemistry
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spelling Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition statesBofill i Villà, Josep M.Ribas Ariño, JordiValero Montero, RosendoAlbareda, GuillermoMoreira, Ibério de Pinho RibeiroQuapp, WolfgangDinàmica molecularAlgorismes computacionalsQuímica físicaMolecular dynamicsComputer algorithmsPhysical and theoretical chemistryAn algorithm to locate transition states on a potential energy surface (PES) is proposed and described. The technique is based on the GAD method where the gradient of the PES is projected into a given direction and also perpendicular to it. In the proposed method, named GAD-CD, the projection is not only applied to the gradient but also to the Hessian matrix. Then, the resulting Hessian matrix is block diagonal. The direction is updated according to the GAD method. Furthermore, to ensure stability and to avoid a high computational cost, a trust region technique is incorporated and the Hessian matrix is updated at each iteration. The performance of the algorithm in comparison with the standard ascent dynamics is discussed for a simple two dimensional model PES. Its efficiency for describing the reaction mechanisms involving small and medium size molecular systems is demonstrated for five molecular systems of interest.American Chemical Society2019info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfhttps://hdl.handle.net/2445/152811Articles publicats en revistes (Química Inorgànica i Orgànica)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésVersió postprint del document publicat a: https://doi.org/10.1021/acs.jctc.8b01061Journal of Chemical Theory and Computation, 2019, vol. 15, num. 10, p. 5426-5439https://doi.org/10.1021/acs.jctc.8b01061info:eu-repo/grantAgreement/EC/H2020/752822(c) American Chemical Society , 2019info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1528112026-05-27T06:46:51Z
dc.title.none.fl_str_mv Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
title Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
spellingShingle Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
Bofill i Villà, Josep M.
Dinàmica molecular
Algorismes computacionals
Química física
Molecular dynamics
Computer algorithms
Physical and theoretical chemistry
title_short Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
title_full Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
title_fullStr Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
title_full_unstemmed Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
title_sort Interplay between the gentlest ascent dynamics method and conjugate directions to locate transition states
dc.creator.none.fl_str_mv Bofill i Villà, Josep M.
Ribas Ariño, Jordi
Valero Montero, Rosendo
Albareda, Guillermo
Moreira, Ibério de Pinho Ribeiro
Quapp, Wolfgang
author Bofill i Villà, Josep M.
author_facet Bofill i Villà, Josep M.
Ribas Ariño, Jordi
Valero Montero, Rosendo
Albareda, Guillermo
Moreira, Ibério de Pinho Ribeiro
Quapp, Wolfgang
author_role author
author2 Ribas Ariño, Jordi
Valero Montero, Rosendo
Albareda, Guillermo
Moreira, Ibério de Pinho Ribeiro
Quapp, Wolfgang
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Dinàmica molecular
Algorismes computacionals
Química física
Molecular dynamics
Computer algorithms
Physical and theoretical chemistry
topic Dinàmica molecular
Algorismes computacionals
Química física
Molecular dynamics
Computer algorithms
Physical and theoretical chemistry
description An algorithm to locate transition states on a potential energy surface (PES) is proposed and described. The technique is based on the GAD method where the gradient of the PES is projected into a given direction and also perpendicular to it. In the proposed method, named GAD-CD, the projection is not only applied to the gradient but also to the Hessian matrix. Then, the resulting Hessian matrix is block diagonal. The direction is updated according to the GAD method. Furthermore, to ensure stability and to avoid a high computational cost, a trust region technique is incorporated and the Hessian matrix is updated at each iteration. The performance of the algorithm in comparison with the standard ascent dynamics is discussed for a simple two dimensional model PES. Its efficiency for describing the reaction mechanisms involving small and medium size molecular systems is demonstrated for five molecular systems of interest.
publishDate 2019
dc.date.none.fl_str_mv 2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/152811
url https://hdl.handle.net/2445/152811
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1021/acs.jctc.8b01061
Journal of Chemical Theory and Computation, 2019, vol. 15, num. 10, p. 5426-5439
https://doi.org/10.1021/acs.jctc.8b01061
info:eu-repo/grantAgreement/EC/H2020/752822
dc.rights.none.fl_str_mv (c) American Chemical Society , 2019
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) American Chemical Society , 2019
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv Articles publicats en revistes (Química Inorgànica i Orgànica)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,301603

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