Temporally coherent backmapping of molecular trajectories from coarse-grained to atomistic resolution

TL;DR

This paper introduces a deep learning method for reconstructing atomistic details from coarse-grained molecular simulations, ensuring temporal coherence and high fidelity in the reconstructed trajectories.

Contribution

It presents a novel deep learning approach using a conditional variational autoencoder that incorporates previous frames for temporally coherent backmapping of molecular trajectories.

Findings

Accurately recovers structural properties of biomolecular systems.

Maintains thermodynamic and kinetic fidelity in reconstructed trajectories.

Demonstrates effectiveness on alanine dipeptide and chignolin.

Abstract

Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation, or parameterized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to produce higher-fidelity atomic reconstructions. In this work we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to non-deterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data.