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Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why
Pinchen Xie1,2, Weinan E3,4
1Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, United States.
Abstract:
A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation-dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.
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