Song Zilin, Ding Ye, Huang Jing
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
J Comput Chem. 2023 Oct 5;44(26):2042-2057. doi: 10.1002/jcc.27178. Epub 2023 Jun 22.
The chain-of-states (CoS) constant advance replicas (CAR) method and its climbing image variant (CI-CAR) for locating minimum energy paths (MEPs) and transition states are reported. The CAR algorithm applies the Lagrange multiplier method for imposing holonomic constraints on a chain-of-replicas, aiming to maintain equal mass-weighted/scaled root-mean-square (RMS) distances between the adjacent replicas by removing the sliding-down displacements contributed by the potential gradients during path optimization. Two contextual regularization schemes with clear geometrical interpretations are implemented to jointly promote high convergence and numerical robustness of the CAR algorithm. We show that the constrained reaction path can be solved normally within 5 steps of Lagrange multiplier updates with remarkably high numerical precision via the CAR approach. The efficacy of the CAR methods is demonstrated by testing on multiple analytical, classical, and quantum mechanical transition paths: the Müller potential, the alanine dipeptide isomerization, the helix unwinding of the VIVITLVMLKKK 12-mer peptide, and the Baker set of reactions. We also explore the potential of applying adaptive momentum (AdaM) optimizers for locating optimal transition paths under complex conformational changes. Most importantly, we discuss extensively the differences and connections between our newly proposed CAR methods and several related methods, with focuses on the reaction path with holonomic constraints (RPCons) approach of Brokaw et al. [J. Chem. Theory Comput. 2009, 5 (8), 2050-2061] and the state-of-the-art string method (SM) of E et al. [J. Chem. Phys. 2007, 126 (16), 164103]. The CAR approach represents a latest update to the general theoretical framework of reaction path finding algorithms in the two-ended CoS regime.
报道了用于定位最小能量路径(MEP)和过渡态的状态链(CoS)恒定前进副本(CAR)方法及其爬坡图像变体(CI-CAR)。CAR算法应用拉格朗日乘数法对副本链施加完整约束,旨在通过消除路径优化过程中由势梯度贡献的下滑位移,来保持相邻副本之间相等的质量加权/缩放均方根(RMS)距离。实施了两种具有清晰几何解释的上下文正则化方案,以共同促进CAR算法的高收敛性和数值稳健性。我们表明,通过CAR方法,在拉格朗日乘数更新的5步之内,约束反应路径通常能够以极高的数值精度得到求解。通过对多个解析、经典和量子力学过渡路径进行测试,证明了CAR方法的有效性:米勒势、丙氨酸二肽异构化、VIVITLVMLKKK 12聚体肽的螺旋解旋以及贝克反应集。我们还探索了应用自适应动量(AdaM)优化器在复杂构象变化下定位最优过渡路径的潜力。最重要的是,我们广泛讨论了新提出的CAR方法与几种相关方法之间的差异和联系,重点关注Brokaw等人[《化学理论计算杂志》2009年,5(8),2050 - 2061]的具有完整约束的反应路径(RPCons)方法以及E等人[《化学物理杂志》2007年,126(16),164103]的最新弦方法(SM)。CAR方法代表了两端CoS体系中反应路径寻找算法一般理论框架的最新更新。