Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm

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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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Autor principal: Ramírez, C.L
Otros Autores: Zeida, A., Jara, G.E, Roitberg, A.E, Martí, M.A
Formato: Capítulo de libro
Lenguaje:Inglés
Publicado: American Chemical Society 2014
Acceso en línea:Registro en Scopus
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100 1 |a Ramírez, C.L. 
245 1 0 |a Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm 
260 |b American Chemical Society  |c 2014 
270 1 0 |m Martí, M.A.; Departamento de Química Biológica, FCEN, UBAArgentina 
506 |2 openaire  |e Política editorial 
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520 3 |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.  |l eng 
593 |a Departamento de Química Inorgánica, Analítica y Química Física, Argentina 
593 |a Departamento de Química Biológica, FCEN, UBA, Buenos Aires, C1428EGA, Argentina 
593 |a Instituto de Química Física de Los Materiales, Medio Ambiente y Energía, UBA-CONICET, Buenos Aires, C1428EGA, Argentina 
593 |a Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, United States 
700 1 |a Zeida, A. 
700 1 |a Jara, G.E. 
700 1 |a Roitberg, A.E. 
700 1 |a Martí, M.A. 
773 0 |d American Chemical Society, 2014  |g v. 10  |h pp. 4609-4617  |k n. 10  |p J. Chem. Theory Comput.  |x 15499618  |t Journal of Chemical Theory and Computation 
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856 4 0 |u https://doi.org/10.1021/ct500672d  |y DOI 
856 4 0 |u https://hdl.handle.net/20.500.12110/paper_15499618_v10_n10_p4609_Ramirez  |y Handle 
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