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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" (2014) Journal of Chemical Theory and Computation. 10(10):4609-4617
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Abstract:

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.

Registro:

Documento: Artículo
Título:Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm
Autor:Ramírez, C.L.; Zeida, A.; Jara, G.E.; Roitberg, A.E.; Martí, M.A.
Filiación:Departamento de Química Inorgánica, Analítica y Química Física, Argentina
Departamento de Química Biológica, FCEN, UBA, Buenos Aires, C1428EGA, Argentina
Instituto de Química Física de Los Materiales, Medio Ambiente y Energía, UBA-CONICET, Buenos Aires, C1428EGA, Argentina
Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, United States
Año:2014
Volumen:10
Número:10
Página de inicio:4609
Página de fin:4617
DOI: http://dx.doi.org/10.1021/ct500672d
Título revista:Journal of Chemical Theory and Computation
Título revista abreviado:J. Chem. Theory Comput.
ISSN:15499618
CODEN:JCTCC
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v10_n10_p4609_Ramirez

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Citas:

---------- APA ----------
Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E. & Martí, M.A. (2014) . Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm. Journal of Chemical Theory and Computation, 10(10), 4609-4617.
http://dx.doi.org/10.1021/ct500672d
---------- CHICAGO ----------
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" . Journal of Chemical Theory and Computation 10, no. 10 (2014) : 4609-4617.
http://dx.doi.org/10.1021/ct500672d
---------- MLA ----------
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" . Journal of Chemical Theory and Computation, vol. 10, no. 10, 2014, pp. 4609-4617.
http://dx.doi.org/10.1021/ct500672d
---------- VANCOUVER ----------
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. J. Chem. Theory Comput. 2014;10(10):4609-4617.
http://dx.doi.org/10.1021/ct500672d