用贝叶斯优化改进粗粒化分子力场,提升特定领域模拟精度。
Refining Coarse-Grained Molecular Topologies: A Bayesian Optimization Approach
- 基于贝叶斯优化调整Martini3力场的键合参数,适配特定应用
- 在保持粗粒化效率的同时,精度接近全原子模拟水平
- 适合需要高精度与高速度平衡的聚合物等领域的分子模拟
分子动力学(MD)模拟对预测大规模分子体系在不同压强和温度下的物理化学性质至关重要。然而,全原子(AA)MD模拟计算成本高昂,促使了粗粒化分子动力学(CGMD)的发展,将原子结构压缩为代表性粗粒化珠子,以降低计算开销但牺牲预测精度。现有方法如基于实验数据校准的CG-Martini,在跨分子类别泛化方面表现良好,却难以针对特定领域实现高精度。本文提出一种新方法,利用贝叶斯优化对通用的Martini3拓扑进行精细化调整,聚焦于特定粗粒化映射下的键合相互作用参数,从而实现针对特定应用的性能优化。我们开发并验证了一种适用于任意聚合度的粗粒化势函数,是该领域的显著进展。所提出的优化势函数基于Martini3框架,目标是在保持CGMD计算效率的同时,达到接近全原子模拟的精度。该方法弥合了多尺度模拟中效率与精度之间的鸿沟,有望加速科学与技术领域中的分子发现过程。
原文摘要 · Abstract (English)
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated with All-Atom (AA) MD simulations have led to the development of Coarse-Grained Molecular Dynamics (CGMD), providing a lower-dimensional compression of the AA structure into representative CG beads, offering reduced computational expense at the cost of predictive accuracy. Existing CGMD methods, such as CG-Martini (calibrated against experimental data), aim to generate an embedding of a topology that sufficiently generalizes across a range of structures. Detrimentally, in attempting to specify parameterization with applicability across molecular classes, it is unable to specialize to domain-specific applications, where sufficient accuracy and computational speed are critical. This work presents a novel approach to optimize derived results from CGMD simulations by refining the general-purpose Martini3 topologies specifically the bonded interaction parameters within a given coarse-grained mapping - for domain-specific applications using Bayesian Optimization methodologies. We have developed and validated a CG potential applicable to any degree of polymerization, representing a significant advancement in the field. Our optimized CG potential, based on the Martini3 framework, aims to achieve accuracy comparable to AAMD while maintaining the computational efficiency of CGMD. This approach bridges the gap between efficiency and accuracy in multiscale molecular simulations, potentially enabling more rapid and cost-effective molecular discovery across various scientific and technological domains.
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