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arXiv · 1904.07177

Coarse-graining Molecular Systems by Spectral Matching

Feliks Nüske·Lorenzo Boninsegna·Cecilia Clementi
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Abstract

Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale systems become computationally tractable. While significant progress has been made in tuning thermodynamic properties of reduced models, it remains a key challenge to ensure that relevant kinetic properties are retained by coarse-grained dynamical systems. In this study, we focus on data-driven methods to preserve the rare-event kinetics of the original system, and make use of their close connection to the low-lying spectrum of the system's generator. Building on work by Crommelin and Vanden-Eijnden, SIAM Multiscale Model. Simul. (2011), we present a general framework, called spectral matching, which directly targets the generator's leading eigenvalue equations when learning parameters for coarse-grained models. We discuss different parametric models for effective dynamics and derive the resulting data-based regression problems. We show that spectral matching can be used to learn effective potentials which retain the slow dynamics, but also to correct the dynamics induced by existing techniques, such as force matching.

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Feliks Nüske, Lorenzo Boninsegna, Cecilia Clementi. 2019-04-15. Coarse-graining Molecular Systems by Spectral Matching. https://doi.org/10.1063/1.5100131

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