##manager.scheduler.building##: Edificio Santa Maria
##manager.scheduler.room##: Auditorio San Agustin
Date: 2019-07-10 12:00 PM – 03:45 PM
Last modified: 2019-06-14
Abstract
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, towards a subset of ligands or in the specific effect of a point mutation, as well as in other problems of biological relevance. 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. This procedure permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution.