Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning
Name
Fu-xiangfu-SM-EECS-2022-thesis.pdf
Description
Thesis PDF
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13.72 MB
Format
Adobe PDF
Checksum (MD5)
feb73f5374221f24ac15cedf89272274
Author(s)
Fu, Xiang
Advisor(s)
Jaakkola, Tommi S.
Date Issued
May 2022
Publisher
Massachusetts Institute of Technology
Abstract
Molecular dynamics (MD) simulation is the workhorse of various scientific domains but is limited by high computational cost. Learning-based force fields have made major progress in accelerating ab-initio MD simulation but are still not fast enough for many real-world applications that require long-time MD simulation. In this paper, we adopt a different machine learning approach where we coarse-grain a physical system using graph clustering, and model the system evolution with a very large time-integration step using graph neural networks. Despite only trained with short MD trajectory data, our learned simulator can generalize to unseen novel systems and simulate for much longer than the training trajectories. Properties requiring 10-100 ns level long-time dynamics can be accurately recovered at several-orders-of-magnitude higher speed than classical force fields. We demonstrate the effectiveness of our method on two realistic complex systems: (1) single-chain coarse-grained polymers in implicit solvent; (2) multi-component Li-ion polymer electrolyte systems.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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