Data-driven molecular modeling with the generalized Langevin equation

J Comput Phys. 2020 Oct 1;418:109633. doi: 10.1016/j.jcp.2020.109633. Epub 2020 Jun 3.

Abstract

The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation (GLE) describes coarse-grained dynamics in reduced dimensions. In spite of playing a crucial role in non-equilibrium dynamics, the memory kernel of the GLE is often ignored because it is difficult to characterize and expensive to solve. To address these issues, we construct a data-driven rational approximation to the GLE. Building upon previous work leveraging the GLE to simulate simple systems, we extend these results to more complex molecules, whose many degrees of freedom and complicated dynamics require approximation methods. We demonstrate the effectiveness of our approximation by testing it against exact methods and comparing observables such as autocorrelation and transition rates.

Keywords: coarse-grained models; data-driven parametrization; dimension reduction; generalized Langevin equation; molecular dynamics.