Rare events explored by molecular simulations and dynamical reweighting

Rare events explored by molecular simulations and dynamical reweighting

Rare events explored by molecular simulations and dynamical reweighting

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The relevant timescales of molecular processes range from femtoseconds to minutes or even days. While timescales up several tens or microseconds can now be modelled by direct molecular simulations (with atomistic force fields), slower processes need to be modelled by biased or enhanced sampling simulations. These slow timescales are particularly relevant for intermolecular interactions ranging from chemical reactions between small molecules to protein-protein binding. I will present two methods to recover the correct kinetics from enhanced sampling simulations. In path reweighting one calculates kinetic properties as path ensemble averages. The weight of each path sampled at a biased potential is rescaled to correct weight at the unbiased molecular potential. I will discuss how to extract  the path weights efficiently form molecular simulations. By discretizing the Fokker-Planck equation of molecular dynamics, one can obtain kinetic models directly from multi-dimensional (free-)energy surfaces and diffusion profile. I will discuss how to meet the challenges that arise from steep and narrow barriers (such as barriers in chemical reactions) and the presence of nonlinear reaction coordinates.
Some useful references:
  •  Donati, Luca, and Bettina G. Keller. « Girsanov reweighting for metadynamics simulations. » The Journal of chemical physics 149.7 (2018): 072335.
  •  Kieninger, Stefanie, and Bettina G. Keller. « Path probability ratios for Langevin dynamics — Exact and approximate. » The Journal of Chemical Physics 154.9 (2021): 094102.
  •  Donati, Luca, Marcus Weber, and Bettina G. Keller. « Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux. » Journal of Physics: Condensed Matter 33.11 (2021): 115902.

Informations complémentaires

Auteur - Bettina Keller (Freie Universität Berlin)

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Date et heure

15 septembre 2022 @ 03:00 PM
 

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