Systems Biology Group Meeting
Topic: QM/MM simulation – Introduction, practicalities and case studies
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations are a popular tool for the investigation of somewhat niche condensed-phase chemical reactions. In a QM/MM simulation, the region of chemical interest is treated with a quantum chemical method at an appropriate level of theory whilst the rest of the system is treated with a molecular mechanics force-field, representing a practical compromise between chemical accuracy and simulation performance. Practical challenges associated with the setup and running of these simulations will be illustrated with examples from unusual chemical systems, such as actinides, in environments as diverse in size as small sugars and serum proteins.