Loferer Markus J, Loeffler Hannes H, Liedl Klaus R
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
J Comput Chem. 2003 Jul 30;24(10):1240-9. doi: 10.1002/jcc.10283.
The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.
本文描述了一种将TURBOMOLE的从头算和密度泛函方法与分子力学程序包CHARMM相结合的混合量子力学-分子力学（QM-MM）方法的实现。已创建一个接口，以允许两个应用程序之间进行数据交换。使用这种方法，可以将TURBOMOLE的高效多处理器功能与作为单处理器应用程序运行的CHARMM一起使用。因此，通过并行运行CPU密集型的量子力学计算，可以利用CHARMM中非并行运行代码的功能，如用于定位鞍点的TRAVEL模块或用于计算二阶导数的VIBRAN。为了测试该方法，使用Hartree-Fock和密度泛函方法以及不同的QM-MM边界对几个小系统进行了研究。此外，还研究了计算效率高的RI-J方法在QM-MM应用中的使用。研究了含有钴的B(12)辅因子，以研究具有大量子力学区域和过渡金属的系统。与纯量子计算相比，所有测试方法的表现都令人满意。此外，还测试了用于表征鞍点的算法在QM-MM问题中的潜在用途。CHARMM的TRAVEL模块已应用于凝聚相中的门舒特金反应，并找到了一个鞍点。通过计算连接反应物、过渡态和产物的最陡下降路径以及计算振动模式，验证了这个鞍点。
