QM/MM

Reading materials

• Chapter 13 of Cramer, C. J. Essentials of Computational Chemistry: Theories and Models, 2nd ed.; John Wiley & Sons, 2013.
• References in the “Molecular Simulation -> QM/MM” folder of the group Zotero library, especially the following reviews:

1. Bramley, G. A.; Beynon, O. T.; Stishenko, P. V.; Logsdail, A. J. The Application of QM/MM Simulations in Heterogeneous Catalysis. Phys. Chem. Chem. Phys. 2023, 10.1039.D2CP04537K.
2. Chung, L. W.; Sameera, W. M. C.; Ramozzi, R.; Page, A. J.; Hatanaka, M.; Petrova, G. P.; Harris, T. V.; Li, X.; Ke, Z.; Liu, F.; Li, H.-B.; Ding, L.; Morokuma, K. The ONIOM Method and Its Applications. Chem. Rev. 2015, 115, 5678–5796.
3. Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems. Angew. Chem. Int. Ed. 2009, 48, 1198–1229.
4. Lin, H.; Truhlar, D. G. QM/MM: What Have We Learned, Where Are We, and Where Do We Go from Here? Theor. Chem. Acc. 2007, 117, 185–199.

Software codes for performing QM/MM

• ChemShell: A copy is uploaded to our group SharePoint folder.
• ONIOM methods in Gaussian.
• GROMACS/CP2K.
• GULP has very good support for shell models for ionic materials and can interface with QMPot, TURBOMOLE, and ABINIT. A copy is uploaded to our group SharePoint folder.
• Tinker (next version) is a molecular mechanics code and can interface with GAMESS-UK and Q-Chem.
• INAQS supports both Born-Oppenheimer, Ehrenfest, and surface hopping (non-adiabatic) dynamics.