用机器学习驱动多尺度分子模拟,让小设备也能跑复杂生物系统模拟。
Machine Learning-driven Multiscale MD Workflows: The Mini-MuMMI Experience
- 基于机器学习构建可跨尺度协调的模拟工作流
- 在毫秒到纳秒级时间尺度上并行运行数千次模拟
- 轻量版支持笔记本运行,拓展至非蛋白模拟场景
计算模型已成为模拟复杂现象的重要手段。为精确刻画如生物分子间相互作用等复杂过程,科学家常采用由多个在不同尺度(从微观到宏观)运行的内部模型组成的多尺度模型。跨时间与空间尺度的衔接历来困难,但新型机器学习方法为此提供了新路径。多尺度模型需大量计算资源及强大工作流管理系统,而将数千个在不同时间尺度运行的分子动力学(MD)模拟在数千节点的并行系统上协同调度极具挑战。本文介绍大规模并行的多尺度机器学习建模基础设施(MuMMI),其可协调毫秒至纳秒尺度的数千次MD模拟。我们提出简化版本mini-MuMMI,专为中等规模超算或甚至笔记本电脑设计,相较原版降低硬件要求。通过研究RAS-RAF膜相互作用验证其有效性,并讨论多尺度工作流泛化面临的挑战,说明mini-MuMMI可推广至非MD领域与更广泛应用。
原文摘要 · Abstract (English)
Computational models have become one of the prevalent methods to model complex phenomena. To accurately model complex interactions, such as detailed biomolecular interactions, scientists often rely on multiscale models comprised of several internal models operating at difference scales, ranging from microscopic to macroscopic length and time scales. Bridging the gap between different time and length scales has historically been challenging but the advent of newer machine learning (ML) approaches has shown promise for tackling that task. Multiscale models require massive amounts of computational power and a powerful workflow management system. Orchestrating ML-driven multiscale studies on parallel systems with thousands of nodes is challenging, the workflow must schedule, allocate and control thousands of simulations operating at different scales. Here, we discuss the massively parallel Multiscale Machine-Learned Modeling Infrastructure (MuMMI), a multiscale workflow management infrastructure, that can orchestrate thousands of molecular dynamics (MD) simulations operating at different timescales, spanning from millisecond to nanosecond. More specifically, we introduce a novel version of MuMMI called "mini-MuMMI". Mini-MuMMI is a curated version of MuMMI designed to run on modest HPC systems or even laptops whereas MuMMI requires larger HPC systems. We demonstrate mini-MuMMI utility by exploring RAS-RAF membrane interactions and discuss the different challenges behind the generalization of multiscale workflows and how mini-MuMMI can be leveraged to target a broader range of applications outside of MD and RAS-RAF interactions.
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