Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics


P. R. Vlachas, J. Zavadlav, M. Praprotnik, and P. Koumoutsakos, “Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics,” J. Chem. Theory Comput. vol. 18, no. 1, pp. 538-549, 2022.


Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the time scales necessary to capture the structural evolution of biomolecules remains a daunting task. In this work, we present a novel framework to advance simulation time scales by up to 3 orders of magnitude by learning the effective dynamics (LED) of molecular systems. LED augments the equation-free methodology by employing a probabilistic mapping between coarse and fine scales using mixture density network (MDN) autoencoders and evolves the non-Markovian latent dynamics using long short-term memory MDNs. We demonstrate the effectiveness of LED in the Müller–Brown potential, the Trp cage protein, and the alanine dipeptide. LED identifies explainable reduced-order representations, i.e., collective variables, and can generate, at any instant, all-atom molecular trajectories consistent with the collective variables. We believe that the proposed framework provides a dramatic increase to simulation capabilities and opens new horizons for the effective modeling of complex molecular systems.

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Last updated on 03/30/2022