F^3low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching
arxiv(2024)
摘要
Molecular dynamics (MD) is a crucial technique for simulating biological
systems, enabling the exploration of their dynamic nature and fostering an
understanding of their functions and properties. To address exploration
inefficiency, emerging enhanced sampling approaches like coarse-graining (CG)
and generative models have been employed. In this work, we propose a
Frame-to-Frame generative model with guided
Flow-matching (F3low) for enhanced sampling, which (a) extends
the domain of CG modeling to the SE(3) Riemannian manifold; (b) retreating CGMD
simulations as autoregressively sampling guided by the former frame via
flow-matching models; (c) targets the protein backbone, offering improved
insights into secondary structure formation and intricate folding pathways.
Compared to previous methods, F3low allows for broader exploration of
conformational space. The ability to rapidly generate diverse conformations via
force-free generative paradigm on SE(3) paves the way toward efficient enhanced
sampling methods.
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