Electronic Structure Topology Associated Domain is Useful to Minimize the Uncertainty of QM/MM Boundary Charge Transfer Effects
| Autor: | Yang, Jiajun, Liu, Fang, Zhang, Dongju, Du, Likai |
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| Rok vydání: | 2018 |
| Předmět: | |
| Druh dokumentu: | Working Paper |
| Popis: | The charge transfer effect is an important component in the physical description of realistic proteins. In the hybrid quantum mechanical-molecular mechanical (QM/MM) simulations, the significant charge transfer between the QM/MM boundaries could lead to the slow convergence problem with very large QM regions. In this work, we will discuss how community structure in complex network (electronic structure topology associated domain) can be used to measure QM/MM boundary effects and how it can provide a different perspective on well established concepts in available QM/MM simulations. The graph theory is employed to provide an useful solution to distinguish the significant charge transfer regions between the core active site and the surrounding protein environment in the QM/MM simulations. According to community detection algorithm for complex network, the charge transfer topology associated domain (ctTAD) is suggested to provide an alternative tool for systematically minimizing the charge transfer effects of QM/MM boundary with minor computational costs. Comment: 32 pages, 11 figures |
| Databáze: | arXiv |
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