Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
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DOI：
10.1039/a909486e
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发表时间：
2000-01-01
影响因子：
3.3
通讯作者：
Thiel, W
中科院分区：
文献类型：
--
作者：
Billeter, SR;Turner, AJ;Thiel, W
在半经验量子化学程序(MNDO)和模块化量子力学/分子力学(QM/MM)程序(ChemShell)的背景下，开发并实现了一种基于混合离域内坐标(HDLC)的线性标度几何优化和过渡态搜索算法。线性缩放是通过分而治之的方法实现的：系统被划分为用户定义的片段，所有坐标操作都在这些片段中专门执行。优化器采用有限内存的准牛顿算法(L-BFGS)进行能量最小化，过渡态搜索采用海森本征模跟踪算法(P-RFO)用于反应核心，L-BFGS算法用于环境搜索。存在从笛卡尔坐标生成内部坐标的冗余集合和HDLC的非冗余集合的自动程序。优化器的输入包括初始笛卡尔几何、系统的碎片化、工作坐标系的选择以及要在笛卡尔和/或内部坐标中施加的任何约束。优化器需要一个外部函数，该函数在给定的笛卡尔几何图形上提供能量和梯度。对具有数千个原子的体系进行了优化，并确定了一个模型酶反应的过渡态。
An algorithm for linear scaling geometry optimisation and transition state search using hybrid delocalised internal coordinates (HDLC) has been developed and implemented in the context of a semiempirical quantum-chemistry program (MNDO) and a modular quantum-mechanical/molecular-mechanical (QM/MM) package (ChemShell). Linear scaling is achieved by a divide-and-conquer approach: the system is partitioned into user-defined fragments, and all coordinate manipulations are performed exclusively within these fragments. The optimiser employs a limited-memory quasi-Newton algorithm (L-BFGS) for energy minimisation, and a microiterative scheme for transition state search using a Hessian eigenmode-following algorithm (P-RFO) for the reaction core and the L-BFGS algorithm for the environment. There are automatic procedures for generating redundant sets of internal coordinates and non-redundant sets of HDLC from Cartesian coordinates. The input to the optimiser consists of the initial Cartesian geometry, the fragmentation of the system, the choice of the working coordinate system, and any constraints to be imposed in Cartesian and/or internal coordinates. The optimiser requires an external function that provides the energy and gradient at a given Cartesian geometry. Systems with thousands of atoms have been optimised, and transition states of a model enzymatic reaction have been determined.