Hybrid molecular dynamics simulations combining Quantum Mechanics and Molecular Mechanics (QM/MM) provide a cost-effective way of studying a large range of chemical processes. The latest version of NAMD presents a native interface to MOPAC, ORCA and, through a script interface, to many QM packages. NAMD users can now combine its enhanced sampling and free energy calculation tools with the latest developments in quantum chemistry. VMD has also been extended, particularly through the QwikMD interface, making it easy to prepare, perform, analyze and visualize QM/MM simulations. QwikMD assists the selection of QM regions while automatically handling bonds connecting QM to MM atoms. Beginners can start QM/MM simulations in a few minutes using pre-set templates, while experienced researchers can easily fine tune any aspect of their QM/MM calculations. The QM/MM interface was employed to probe t-RNA charging mechanism, as well as the reaction mechanism of the respiratory complex I.

NAMD and VMD combined for easy and fast QM/MM simulations

255th National Meeting (2018)

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