Seminar by Dr. Riccardo Capelli

University of Milan (Italy)

Biased molecular simulations of non-equilibrium protein dynamics

Inferential methods can be used to integrate experimental information in molecular simulations. The maximum entropy principle provides a framework for integrating equilibrium experimental data in molecular dynamics and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such principle. We show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus could allow us to integrate time-resolved data in molecular dynamics simulations. Particularly relevant is the fact that this approach not only allows us to correct force field parametrization, but the experimental data can also be used to speed up the simulation.