Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4.
J Comput Chem. 2010 Apr 15;31(5):1015-23. doi: 10.1002/jcc.21387.
We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi-particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force-field (CHARMM27) or a polarizable force-field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual-thermostat method and the VV2 integrator to run molecular dynamics simulations.
我们提出了一种新的QM/MM 接口，用于快速高效地模拟有机和生物分子。CHARMM/deMon 接口已经开发并经过测试，可用于多粒子系统的最小化和原子模拟。该 QM/MM 接口的当前功能包括分子动力学的可读性，经过测试与使用双拓扑/单坐标方法的自由能微扰模拟（FEP）兼容。当前的耦合方案使用链接原子，但计划进一步扩展代码以纳入其他可用方案。我们报告了不同理论水平对 QM 区域处理的性能，而 MM 区域则由经典力场（CHARMM27）或基于简单 Drude 模型的极化力场表示。当前的 QM/MM 实现可以与双恒温器方法和 VV2 积分器耦合，以运行分子动力学模拟。
