GPU accelerated implementation of density functional theory for hybrid QM/MM simulations

Autores
Nitsche, Matias Alejandro; Ferreria, Manuel; Mocskos, Esteban Eduardo; González Lebrero, Mariano Camilo
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density functional theory. This development is optimized for performing hybrid molecular dynamics simulations by making use of graphic processors (GPU) for the most computationally demanding parts (exchange-correlation terms). The proposed implementation is able to take advantage of modern GPUs achieving acceleration in relevant portions between 20 to 30 times faster than the CPU version. The presented code was extensively tested, both in terms of numerical quality and performance over systems of different size and composition.
Fil: Nitsche, Matias Alejandro. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ferreria, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; Argentina
Fil: Mocskos, Esteban Eduardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; Argentina
Fil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; Argentina
Materia
Dft
Qm/Mm
Gpu
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:11336/17976
Acceder
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network_name_str CONICET Digital (CONICET)
spelling GPU accelerated implementation of density functional theory for hybrid QM/MM simulationsNitsche, Matias AlejandroFerreria, ManuelMocskos, Esteban EduardoGonzález Lebrero, Mariano CamiloDftQm/MmGpuhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density functional theory. This development is optimized for performing hybrid molecular dynamics simulations by making use of graphic processors (GPU) for the most computationally demanding parts (exchange-correlation terms). The proposed implementation is able to take advantage of modern GPUs achieving acceleration in relevant portions between 20 to 30 times faster than the CPU version. The presented code was extensively tested, both in terms of numerical quality and performance over systems of different size and composition.Fil: Nitsche, Matias Alejandro. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ferreria, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; ArgentinaFil: Mocskos, Esteban Eduardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; ArgentinaFil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaAmerican Chemical Society2014-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/17976Nitsche, Matias Alejandro; Ferreria, Manuel; Mocskos, Esteban Eduardo; González Lebrero, Mariano Camilo; GPU accelerated implementation of density functional theory for hybrid QM/MM simulations; American Chemical Society; Journal Of Chemical Theory And Computation; 10; 3; 2-2014; 959-9671549-9618enginfo:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/ct400308ninfo:eu-repo/semantics/altIdentifier/doi/10.1021/ct400308ninfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:02:21Zoai:ri.conicet.gov.ar:11336/17976instacron: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:34982025-09-10 13:02:22.274CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
title GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
spellingShingle GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
Nitsche, Matias Alejandro
Dft
Qm/Mm
Gpu
title_short GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
title_full GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
title_fullStr GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
title_full_unstemmed GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
title_sort GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
dc.creator.none.fl_str_mv Nitsche, Matias Alejandro
Ferreria, Manuel
Mocskos, Esteban Eduardo
González Lebrero, Mariano Camilo
author Nitsche, Matias Alejandro
author_facet Nitsche, Matias Alejandro
Ferreria, Manuel
Mocskos, Esteban Eduardo
González Lebrero, Mariano Camilo
author_role author
author2 Ferreria, Manuel
Mocskos, Esteban Eduardo
González Lebrero, Mariano Camilo
author2_role author
author
author
dc.subject.none.fl_str_mv Dft
Qm/Mm
Gpu
topic Dft
Qm/Mm
Gpu
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density functional theory. This development is optimized for performing hybrid molecular dynamics simulations by making use of graphic processors (GPU) for the most computationally demanding parts (exchange-correlation terms). The proposed implementation is able to take advantage of modern GPUs achieving acceleration in relevant portions between 20 to 30 times faster than the CPU version. The presented code was extensively tested, both in terms of numerical quality and performance over systems of different size and composition.
Fil: Nitsche, Matias Alejandro. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ferreria, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; Argentina
Fil: Mocskos, Esteban Eduardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; Argentina
Fil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; Argentina
description The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density functional theory. This development is optimized for performing hybrid molecular dynamics simulations by making use of graphic processors (GPU) for the most computationally demanding parts (exchange-correlation terms). The proposed implementation is able to take advantage of modern GPUs achieving acceleration in relevant portions between 20 to 30 times faster than the CPU version. The presented code was extensively tested, both in terms of numerical quality and performance over systems of different size and composition.
publishDate 2014
dc.date.none.fl_str_mv 2014-02
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/11336/17976
Nitsche, Matias Alejandro; Ferreria, Manuel; Mocskos, Esteban Eduardo; González Lebrero, Mariano Camilo; GPU accelerated implementation of density functional theory for hybrid QM/MM simulations; American Chemical Society; Journal Of Chemical Theory And Computation; 10; 3; 2-2014; 959-967
1549-9618
url http://hdl.handle.net/11336/17976
identifier_str_mv Nitsche, Matias Alejandro; Ferreria, Manuel; Mocskos, Esteban Eduardo; González Lebrero, Mariano Camilo; GPU accelerated implementation of density functional theory for hybrid QM/MM simulations; American Chemical Society; Journal Of Chemical Theory And Computation; 10; 3; 2-2014; 959-967
1549-9618
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/ct400308n
info:eu-repo/semantics/altIdentifier/doi/10.1021/ct400308n
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
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 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 12.993085

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