Super-resolution in Molecular Dynamics Trajectory Reconstruction with Bi-Directional Neural Networks

• URL: http://arxiv.org/abs/2201.01195v1
• Date: Sun, 2 Jan 2022 23:00:30 GMT
• Title: Super-resolution in Molecular Dynamics Trajectory Reconstruction with Bi-Directional Neural Networks
• Authors: Ludwig Winkler and Klaus-Robert M\"uller and Huziel E. Sauceda
• Abstract summary: We explore different machine learning (ML) methodologies to increase the resolution of molecular dynamics trajectories on-demand within a post-processing step. We have found that Bi-LSTMs are the best performing models; by utilizing the local time-symmetry of thermostated trajectories they can even learn long-range correlations and display high robustness to noisy dynamics across molecular complexity.
• Score: 0.0
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a computationally expensive process, for example, when running $ab-initio$ simulations. Hence, repeating such calculations to either obtain more accurate thermodynamics or to get a higher resolution in the dynamics generated by a fine-grained quantum interaction can be time- and computationally-consuming. In this work, we explore different machine learning (ML) methodologies to increase the resolution of molecular dynamics trajectories on-demand within a post-processing step. As a proof of concept, we analyse the performance of bi-directional neural networks such as neural ODEs, Hamiltonian networks, recurrent neural networks and LSTMs, as well as the uni-directional variants as a reference, for molecular dynamics simulations (here: the MD17 dataset). We have found that Bi-LSTMs are the best performing models; by utilizing the local time-symmetry of thermostated trajectories they can even learn long-range correlations and display high robustness to noisy dynamics across molecular complexity. Our models can reach accuracies of up to 10$^{-4}$ angstroms in trajectory interpolation, while faithfully reconstructing several full cycles of unseen intricate high-frequency molecular vibrations, rendering the comparison between the learned and reference trajectories indistinguishable. The results reported in this work can serve (1) as a baseline for larger systems, as well as (2) for the construction of better MD integrators.

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