Testing convergence of different free-energy methods in a simple analytical system with hidden barriers

Autores
Paz, Sergio Alexis; Abrams, Cameron
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.
Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Departamento de Química Teórica y Computacional; Argentina
Fil: Abrams, Cameron. Drexel University; Estados Unidos
Materia
ADAPTIVE-BIASING FORCE ALGORITHM
METADYNAMICS
MOLECULAR DYNAMICS
ON-THE-FLY PARAMETERIZATION
TEMPERATUREACCELERATION
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:11336/86336
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/86336
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Testing convergence of different free-energy methods in a simple analytical system with hidden barriersPaz, Sergio AlexisAbrams, CameronADAPTIVE-BIASING FORCE ALGORITHMMETADYNAMICSMOLECULAR DYNAMICSON-THE-FLY PARAMETERIZATIONTEMPERATUREACCELERATIONhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Departamento de Química Teórica y Computacional; ArgentinaFil: Abrams, Cameron. Drexel University; Estados UnidosMDPI Multidisciplinary Digital Publishing Institute2018-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/86336Paz, Sergio Alexis; Abrams, Cameron; Testing convergence of different free-energy methods in a simple analytical system with hidden barriers; MDPI Multidisciplinary Digital Publishing Institute; Computation; 6; 2; 3-20182079-3197CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/2079-3197/6/2/27info:eu-repo/semantics/altIdentifier/doi/10.3390/computation6020027info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:39:33Zoai:ri.conicet.gov.ar:11336/86336instacron: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 10:39:33.276CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
title Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
spellingShingle Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
Paz, Sergio Alexis
ADAPTIVE-BIASING FORCE ALGORITHM
METADYNAMICS
MOLECULAR DYNAMICS
ON-THE-FLY PARAMETERIZATION
TEMPERATUREACCELERATION
title_short Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
title_full Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
title_fullStr Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
title_full_unstemmed Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
title_sort Testing convergence of different free-energy methods in a simple analytical system with hidden barriers
dc.creator.none.fl_str_mv Paz, Sergio Alexis
Abrams, Cameron
author Paz, Sergio Alexis
author_facet Paz, Sergio Alexis
Abrams, Cameron
author_role author
author2 Abrams, Cameron
author2_role author
dc.subject.none.fl_str_mv ADAPTIVE-BIASING FORCE ALGORITHM
METADYNAMICS
MOLECULAR DYNAMICS
ON-THE-FLY PARAMETERIZATION
TEMPERATUREACCELERATION
topic ADAPTIVE-BIASING FORCE ALGORITHM
METADYNAMICS
MOLECULAR DYNAMICS
ON-THE-FLY PARAMETERIZATION
TEMPERATUREACCELERATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.
Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Departamento de Química Teórica y Computacional; Argentina
Fil: Abrams, Cameron. Drexel University; Estados Unidos
description In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.
publishDate 2018
dc.date.none.fl_str_mv 2018-03
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/11336/86336
Paz, Sergio Alexis; Abrams, Cameron; Testing convergence of different free-energy methods in a simple analytical system with hidden barriers; MDPI Multidisciplinary Digital Publishing Institute; Computation; 6; 2; 3-2018
2079-3197
CONICET Digital
CONICET
url http://hdl.handle.net/11336/86336
identifier_str_mv Paz, Sergio Alexis; Abrams, Cameron; Testing convergence of different free-energy methods in a simple analytical system with hidden barriers; MDPI Multidisciplinary Digital Publishing Institute; Computation; 6; 2; 3-2018
2079-3197
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/2079-3197/6/2/27
info:eu-repo/semantics/altIdentifier/doi/10.3390/computation6020027
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 MDPI Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv MDPI Multidisciplinary Digital Publishing Institute
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 13.070432

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