论文标题
QM/mm的机器学习凝结相系统的分子动力学模拟
Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems
论文作者
论文摘要
已经开发了量子力学/分子力学(QM/mm)分子动力学(MD)模拟来模拟分子系统,其中需要明确描述电子结构的变化。但是,与完全经典的模拟相比,QM/MM MD模拟在计算上昂贵,因为所有价电子都经过明确处理,并且需要进行自洽场(SCF)程序。最近,已经提出了用机器学习(ML)模型替换QM描述的方法。但是,由于远距离相互作用,凝结相系统对这些方法构成了挑战。在这里,我们建立了一个工作流,该工作流将MM环境作为元素类型(在高维神经网络电位(HDNNP)中)中。拟合的HDNNP用静电嵌入方案描述了QM颗粒的潜在能量表面。因此,MM颗粒从极化QM颗粒中感觉到力。为了达到化学精度,我们发现即使是简单的系统也需要具有强梯度正则化,大量数据点和大量参数的模型。为了解决这个问题,我们将方法扩展到了Delta学习方案,其中ML模型了解参考方法(DFT)和较便宜的半经验方法(DFTB)之间的差异。我们表明,这种方案达到了DFT参考方法的准确性,同时需要明显更少的参数。此外,Delta学习方案能够在1.4 nm的临界值中正确融合长期相互作用。通过对水中的视黄酸进行MD模拟以及S-腺苷晶元与胞嘧啶在水中的相互作用进行验证。提出的结果表明,Delta-Learning是(QM)ML/MM MD MD模拟的一种有希望的方法。
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD simulations are computationally expensive compared to fully classical simulations as all valence electrons are treated explicitly and a self-consistent field (SCF) procedure is required. Recently, approaches have been proposed to replace the QM description with machine learned (ML) models. However, condensed-phase systems pose a challenge for these approaches due to long-range interactions. Here, we establish a workflow, which incorporates the MM environment as an element type in a high-dimensional neural network potential (HDNNP). The fitted HDNNP describes the potential-energy surface of the QM particles with an electrostatic embedding scheme. Thus, the MM particles feel a force from the polarized QM particles. To achieve chemical accuracy, we find that even simple systems require models with a strong gradient regularization, a large number of data points, and a substantial number of parameters. To address this issue, we extend our approach to a delta-learning scheme, where the ML model learns the difference between a reference method (DFT) and a cheaper semi-empirical method (DFTB). We show that such a scheme reaches the accuracy of the DFT reference method, while requiring significantly less parameters. Furthermore, the delta-learning scheme is capable of correctly incorporating long-range interactions within a cutoff of 1.4 nm. It is validated by performing MD simulations of retinoic acid in water and the interaction between S-adenoslymethioniat with cytosine in water. The presented results indicate that delta-learning is a promising approach for (QM)ML/MM MD simulations of condensed-phase systems.