IC   26529
INSTITUTO DE CALCULO REBECA CHEREP DE GUBER
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
Lessons learned about steered molecular dynamics simulations and free energy calculations
Autor/es:
BOECHI LEONARDO
Lugar:
Cordoba
Reunión:
Congreso; VII MACI 2019; 2019
Institución organizadora:
ASAMACI
Resumen:
The calculation of free energy profiles is central in understanding differential enzy- matic 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.