Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm

The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accura...

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Autores principales: Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E., Martí, M.A.
Formato: JOUR
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_15499618_v10_n10_p4609_Ramirez
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id todo:paper_15499618_v10_n10_p4609_Ramirez
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spelling todo:paper_15499618_v10_n10_p4609_Ramirez2023-10-03T16:23:16Z Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm Ramírez, C.L. Zeida, A. Jara, G.E. Roitberg, A.E. Martí, M.A. The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski;s Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes. © 2014 American Chemical Society. Fil:Ramírez, C.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Jara, G.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15499618_v10_n10_p4609_Ramirez
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
description The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski;s Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes. © 2014 American Chemical Society.
format JOUR
author Ramírez, C.L.
Zeida, A.
Jara, G.E.
Roitberg, A.E.
Martí, M.A.
spellingShingle Ramírez, C.L.
Zeida, A.
Jara, G.E.
Roitberg, A.E.
Martí, M.A.
Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
author_facet Ramírez, C.L.
Zeida, A.
Jara, G.E.
Roitberg, A.E.
Martí, M.A.
author_sort Ramírez, C.L.
title Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
title_short Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
title_full Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
title_fullStr Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
title_full_unstemmed Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
title_sort improving efficiency in smd simulations through a hybrid differential relaxation algorithm
url http://hdl.handle.net/20.500.12110/paper_15499618_v10_n10_p4609_Ramirez
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AT jarage improvingefficiencyinsmdsimulationsthroughahybriddifferentialrelaxationalgorithm
AT roitbergae improvingefficiencyinsmdsimulationsthroughahybriddifferentialrelaxationalgorithm
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