Shajan Akhil, Manathunga Madushanka, Götz Andreas W, Merz Kenneth M
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.
J Chem Theory Comput. 2023 Nov 14;19(21):7533-7541. doi: 10.1021/acs.jctc.3c00188. Epub 2023 Oct 23.
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and energy calculations. The findings demonstrate how the choice of the coordinate system influences the optimization process to reach an equilibrium structure. With fewer steps, internal coordinates outperform Cartesian coordinates, while the choice of the initial Hessian and Hessian update method in quasi-Newton approaches made by different optimization algorithms also contributes to the rate of convergence. Furthermore, an available open-source machine learning method based on Gaussian process regression (GPR) was evaluated for energy minimizations over surrogate potential energy surfaces with both Cartesian and internal coordinates with internal coordinates outperforming Cartesian. Overall, geomeTRIC and DL-FIND with their default optimization method as well as with the GPR-based model using Hartree-Fock theory with the 6-31G** basis set needed a comparable number of geometry optimization steps to the approach of Baker using a unit matrix as the initial Hessian to reach the optimized geometry. On the other hand, the Berny and Sella offerings in ASE outperformed the other algorithms. Based on this, we recommend using the file-based approaches, ASE/Berny and ASE/Sella, for large-scale optimization efforts, while if using a single executable is preferable, we now distribute QUICK integrated with DL-FIND.
基于从30个有机分子的贝克测试集获得的起始结构进行的一系列能量最小化,对各种与开源量子相互作用计算内核(QUICK)程序接口以进行梯度和能量计算的开源几何优化代码进行了比较。研究结果表明了坐标系的选择如何影响优化过程以达到平衡结构。在步数较少的情况下,内部坐标优于笛卡尔坐标,而不同优化算法在拟牛顿法中对初始海森矩阵和海森矩阵更新方法的选择也有助于收敛速度。此外,还评估了一种基于高斯过程回归(GPR)的可用开源机器学习方法,用于在笛卡尔坐标和内部坐标的替代势能面上进行能量最小化,其中内部坐标优于笛卡尔坐标。总体而言,使用其默认优化方法以及使用基于GPR的模型(采用哈特里 - 福克理论和6 - 31G**基组)的geomeTRIC和DL - FIND,与贝克使用单位矩阵作为初始海森矩阵的方法相比,达到优化几何结构所需的几何优化步数相当。另一方面,ASE中的Berny和Sella方法优于其他算法。基于此,我们建议在大规模优化工作中使用基于文件的方法ASE/Berny和ASE/Sella,而如果更倾向于使用单个可执行文件,我们现在发布与DL - FIND集成的QUICK。