Likelihood-based non-Markovian models from molecular dynamics

Abstract

We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from chemical reactions in solution to conformational changes in biomolecules or phase transitions in condensed matter systems. The standard Markovian approximation often breaks down due to the lack of a proper separation of time scales and memory effects must be taken into account. Using a parametrization based on hidden auxiliary variables, we obtain a generalized Langevin equation by maximizing the statistical likelihood of the observed trajectories. Both the memory kernel and random noise are correctly recovered by this procedure. This data-driven approach provides a reduced dynamical model for multidimensional collective variables, enabling the accurate sampling of their long-time dynamical properties at a computational cost drastically reduced with respect to all-atom numerical simulations. The present strategy, based on the reproduction of the dynamics of trajectories rather than the memory kernel or the velocity-autocorrelation function, conveniently provides other observables beyond these two, including e.g. stationary currents in non-equilibrium situations, or the distribution of first passage times between metastable states.

12 pages, 7 figures

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Cited by in corpus (12)

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• Towards a Benchmark for Markov State Models: The Folding of HP35
• Data-driven construction of stochastic reduced dynamics encoded with non-Markovian features
• Accurate Memory Kernel Extraction from Discretized Time Series Data
• Free Energy Landscapes, Diffusion Coefficients, and Kinetic Rates from Transition Paths
• Memory effects in colloidal motion under confinement and driving
• Accurate estimates of dynamical statistics using memory
• Parameter Inference for Degenerate Diffusion Processes
• Efficient spectra from atomistic simulation: a generalized master equation study of the air-water interface
• Position-dependent memory kernel in generalized Langevin equations: theory and numerical estimation
• Weak-Memory Dynamics in Discrete Time