Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

Autores
Seonah, Kim; Orendt, Anita M.; Ferraro, Marta Beatriz; Facelli, Julio C.
Año de publicación
2009
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc.
Fil: Seonah, Kim. University of Utah; Estados Unidos
Fil: Orendt, Anita M.. University of Utah; Estados Unidos
Fil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina
Fil: Facelli, Julio C.. University of Utah; Estados Unidos
Materia
Crystal Structure Prediction
Force Fields
Gaff
Genetic Algorithms
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/60760
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/60760
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force fieldSeonah, KimOrendt, Anita M.Ferraro, Marta BeatrizFacelli, Julio C.Crystal Structure PredictionForce FieldsGaffGenetic Algorithmshttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc.Fil: Seonah, Kim. University of Utah; Estados UnidosFil: Orendt, Anita M.. University of Utah; Estados UnidosFil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; ArgentinaFil: Facelli, Julio C.. University of Utah; Estados UnidosJohn Wiley & Sons Inc2009-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/60760Seonah, Kim; Orendt, Anita M.; Ferraro, Marta Beatriz; Facelli, Julio C.; Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field; John Wiley & Sons Inc; Journal Of Computational Chemistry; 30; 13; 10-2009; 1973-19850192-8651CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.21189info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21189info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:55:45Zoai:ri.conicet.gov.ar:11336/60760instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:55:45.791CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
spellingShingle Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
Seonah, Kim
Crystal Structure Prediction
Force Fields
Gaff
Genetic Algorithms
title_short Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_full Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_fullStr Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_full_unstemmed Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_sort Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
dc.creator.none.fl_str_mv Seonah, Kim
Orendt, Anita M.
Ferraro, Marta Beatriz
Facelli, Julio C.
author Seonah, Kim
author_facet Seonah, Kim
Orendt, Anita M.
Ferraro, Marta Beatriz
Facelli, Julio C.
author_role author
author2 Orendt, Anita M.
Ferraro, Marta Beatriz
Facelli, Julio C.
author2_role author
author
author
dc.subject.none.fl_str_mv Crystal Structure Prediction
Force Fields
Gaff
Genetic Algorithms
topic Crystal Structure Prediction
Force Fields
Gaff
Genetic Algorithms
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc.
Fil: Seonah, Kim. University of Utah; Estados Unidos
Fil: Orendt, Anita M.. University of Utah; Estados Unidos
Fil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina
Fil: Facelli, Julio C.. University of Utah; Estados Unidos
description This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc.
publishDate 2009
dc.date.none.fl_str_mv 2009-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/60760
Seonah, Kim; Orendt, Anita M.; Ferraro, Marta Beatriz; Facelli, Julio C.; Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field; John Wiley & Sons Inc; Journal Of Computational Chemistry; 30; 13; 10-2009; 1973-1985
0192-8651
CONICET Digital
CONICET
url http://hdl.handle.net/11336/60760
identifier_str_mv Seonah, Kim; Orendt, Anita M.; Ferraro, Marta Beatriz; Facelli, Julio C.; Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field; John Wiley & Sons Inc; Journal Of Computational Chemistry; 30; 13; 10-2009; 1973-1985
0192-8651
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.21189
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21189
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv John Wiley & Sons Inc
publisher.none.fl_str_mv John Wiley & Sons Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.069144

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