DIMOS框架让分子模拟兼具速度与可微性,支持机器学习势函数与经典力场混合使用。
Fast, Modular, and Differentiable Framework for Machine Learning-Enhanced Molecular Simulations
- 采用模块化设计,融合机器学习与经典力场,实现端到端可微
- 系统规模增大时线性扩展,速度比同类框架快170倍
- 可优化蒙特卡洛采样参数,使模拟加速3倍,适合材料与生物模拟研究
我们提出一个端到端可微的分子模拟框架DIMOS,适用于分子动力学和蒙特卡洛模拟。该框架能便捷集成基于机器学习的原子间势函数,并实现经典力场(包括高效的粒子网格埃伦费斯特方法)。得益于其模块化设计,经典方法与机器学习方法可轻松结合形成混合描述(ML/MM)。框架支持高效的邻近列表与约束算法,允许更大的时间步长,推动了手工优化模拟引擎与基于PyTorch实现灵活性之间的差距缩小。由于系统规模增加时由二次复杂度变为线性复杂度,与另一全可微框架相比,经典力场模拟速度最高提升170倍。可微性优势通过基于哈密顿蒙特卡洛(HMC)的马尔可夫链蒙特卡洛模拟中提案分布的端到端优化得到验证:使用优化后的参数,模拟速度较手动设定参数提升3倍。代码已公开于https://github.com/nec-research/DIMOS。
原文摘要 · Abstract (English)
We present an end-to-end differentiable molecular simulation framework (DIMOS) for molecular dynamics and Monte Carlo simulations. DIMOS easily integrates machine-learning-based interatomic potentials and implements classical force fields including an efficient implementation of particle-mesh Ewald. Thanks to its modularity, both classical and machine-learning-based approaches can be easily combined into a hybrid description of the system (ML/MM). By supporting key molecular dynamics features such as efficient neighborlists and constraint algorithms for larger time steps, the framework makes steps in bridging the gap between hand-optimized simulation engines and the flexibility of a \verb|PyTorch| implementation. We show that due to improved linear instead of quadratic scaling as function of system size DIMOS is able to obtain speed-up factors of up to $170\times$ for classical force field simulations against another fully differentiable simulation framework. The advantage of differentiability is demonstrated by an end-to-end optimization of the proposal distribution in a Markov Chain Monte Carlo simulation based on Hamiltonian Monte Carlo (HMC). Using these optimized simulation parameters a $3\times$ acceleration is observed in comparison to ad-hoc chosen simulation parameters. The code is available at https://github.com/nec-research/DIMOS.
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