Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks (2204.10348v3)

Abstract: Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for many real-world applications due to slow inference for large systems and small time steps (femtosecond-level). We aim to address these challenges by learning a multi-scale graph neural network that directly simulates coarse-grained MD with a very large time step (nanosecond-level) and a novel refinement module based on diffusion models to mitigate simulation instability. The effectiveness of our method is demonstrated in two complex systems: single-chain coarse-grained polymers and multi-component Li-ion polymer electrolytes. For evaluation, we simulate trajectories much longer than the training trajectories for systems with different chemical compositions that the model is not trained on. Structural and dynamical properties can be accurately recovered at several orders of magnitude higher speed than classical force fields by getting out of the femtosecond regime.

• The paper introduces ML-TCGMD, a framework that simulates molecular dynamics at coarse scales using multi-scale graph networks for extended time integration.
• It employs a fully differentiable architecture with embedding, dynamics, and optional score graph neural networks to bypass costly force calculations.
• Experiments on polymers and Li-ion electrolytes show speedups of 10³ to 10⁴, demonstrating efficient and transferable dynamics prediction.

An Overview of "Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-scale Graph Networks"

The paper "Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-scale Graph Networks" introduces a novel computational approach that addresses the resource-intensive nature of molecular dynamics (MD) simulations, specifically those that require extended time integrations for complex systems such as polymers and proteins. The authors propose a multi-scale graph neural network model, which significantly enhances the efficiency of simulating coarse-grained molecular dynamics without the need for detailed force computations.

Technical Synopsis

The proposed method, named ML-TCGMD, employs a fully differentiable architecture consisting of an Embedding Graph Neural Network (GNN), a Dynamics GNN, and an optional Score GNN for stability refinement. The principal innovation is the direct simulation at coarse scales with extended time steps, reaching up to the nanosecond level, thereby transcending the traditional femtosecond integration constraints typical in MD simulations. This approach effectively reduces computational costs while maintaining accuracy in simulating dynamic and structural properties.

The model is trained using ground truth MD simulations represented as fine-level graphs, which are then transformed into coarse-level graph representations via a graph clustering algorithm. These coarse-grained representations allow the model to bypass computationally expensive force calculations, simulating instead at a high time integration step. A unique feature of this model is its ability to generalize the learned dynamics to new chemical compositions and longer time scales than those encountered during training.

Key Results

The effectiveness of the ML-TCGMD is demonstrated through its application to two complex systems: single-chain coarse-grained polymers and multi-component Li-ion polymer electrolytes. In these experiments, the proposed model achieves a significant speedup, ranging from $10^3$ to $10^4$ in wall-clock time, compared to traditional MD simulations with classical force fields. Specifically:

1. Single-chain Polymers: The model successfully predicts the squared radius of gyration, structural, and long-time dynamical properties, outperforming supervised learning baselines, which suffer from high variance predictions due to shorter training trajectories.
2. Li-ion Polymer Electrolytes: The approach provides accurate estimations of ion transport properties, illustrating its ability to efficiently simulate MD over systems with thousands of atoms.

Implications and Future Directions

The implications of this work are twofold: practical and theoretical. Practically, the model offers a computationally feasible means for conducting high-throughput screenings and large-scale simulations, paving the way for advancements in the paper and design of complex molecular systems. Theoretically, it shifts the paradigm of MD simulations from force computation to learning-based trajectory prediction, inviting further investigation into coarse-grained modeling parameters and historical dependence in dynamics prediction.

Looking ahead, one promising direction is the integration of spatial-dimensional informatics into the coarse-graining process to target specific properties more effectively, thus optimizing the trade-off between granularity and computational efficiency. Additionally, exploring active learning techniques could further enhance the model's applicability across different domains, potentially improving the accuracy of system property predictions.

Overall, the ML-TCGMD framework demonstrated in this paper constitutes a significant contribution to the field of molecular simulations, providing a scalable, efficient, and adaptable solution to a class of problems that have traditionally been limited by computational cost.