Artículo
Lessons learned about steered molecular dynamics simulations and free energy calculations
Boubeta, Fernando Martín
; Contestín García, Rocío María; Lorenzo, Ezequiel Norberto; Boechi, Leonardo
; Estrin, Dario Ariel
; Sued, Raquel Mariela
; Arrar, Mehrnoosh
Fecha de publicación:
01/2019
Editorial:
Wiley Blackwell Publishing, Inc
Revista:
Chemical Biology & Drug Design
ISSN:
1747-0277
Idioma:
Inglés
Tipo de recurso:
Artículo publicado
Clasificación temática:
Resumen
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.
Palabras clave:
FREE ENERGY
,
JARZYNSKI
,
MAXIMUM LIKELIHOOD
,
STEERED MOLECULAR DYNAMICS
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Articulos (IC)
Articulos de INSTITUTO DE CALCULO
Articulos de INSTITUTO DE CALCULO
Articulos(INQUIMAE)
Articulos de INST.D/QUIM FIS D/L MATERIALES MEDIOAMB Y ENERGIA
Articulos de INST.D/QUIM FIS D/L MATERIALES MEDIOAMB Y ENERGIA
Citación
Boubeta, Fernando Martín; Contestín García, Rocío María; Lorenzo, Ezequiel Norberto; Boechi, Leonardo; Estrin, Dario Ariel; et al.; Lessons learned about steered molecular dynamics simulations and free energy calculations; Wiley Blackwell Publishing, Inc; Chemical Biology & Drug Design; 93; 6; 1-2019; 1129-1138
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