Artículo

Boubeta, F.M.; Contestín García, R.M.; Lorenzo, E.N.; Boechi, L.; Estrin, D.; Sued, M.; Arrar, M."Lessons learned about steered molecular dynamics simulations and free energy calculations" (2019) Chemical Biology and Drug Design
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Abstract:

The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution. © 2019 John Wiley & Sons A/S

Registro:

Documento: Artículo
Título:Lessons learned about steered molecular dynamics simulations and free energy calculations
Autor:Boubeta, F.M.; Contestín García, R.M.; Lorenzo, E.N.; Boechi, L.; Estrin, D.; Sued, M.; Arrar, M.
Filiación:CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:free energy; Jarzynski; maximum likelihood; steered molecular dynamics
Año:2019
DOI: http://dx.doi.org/10.1111/cbdd.13485
Handle:http://hdl.handle.net/20.500.12110/paper_17470277_v_n_p_Boubeta
Título revista:Chemical Biology and Drug Design
Título revista abreviado:Chem. Biol. Drug Des.
ISSN:17470277
CODEN:CBDDA
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17470277_v_n_p_Boubeta

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Citas:

---------- APA ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M. & Arrar, M. (2019) . Lessons learned about steered molecular dynamics simulations and free energy calculations. Chemical Biology and Drug Design.
http://dx.doi.org/10.1111/cbdd.13485
---------- CHICAGO ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. "Lessons learned about steered molecular dynamics simulations and free energy calculations" . Chemical Biology and Drug Design (2019).
http://dx.doi.org/10.1111/cbdd.13485
---------- MLA ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. "Lessons learned about steered molecular dynamics simulations and free energy calculations" . Chemical Biology and Drug Design, 2019.
http://dx.doi.org/10.1111/cbdd.13485
---------- VANCOUVER ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. Lessons learned about steered molecular dynamics simulations and free energy calculations. Chem. Biol. Drug Des. 2019.
http://dx.doi.org/10.1111/cbdd.13485