Open Conference Systems, StatPhys 27 Main Conference

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Lessons learned about the use of steered molecular dynamics simulations in the calculation of free energy profiles
Mehrnoosh Arrar, Fernando Boubeta, Ezequiel Lorenzo, Rocío Contestin Garcia, Maria Eugenia Szretter, Dario Estrin, Mariela Sued, Daniela Rodriguez, Leonardo Boechi

##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.