Best Practices in QM/MM Simulation of Biomolecular Systems
This guide provides researchers, especially those new to QM/MM simulation of biomolecular systems, with advice on relevant best practices considered to be important by the organisers and speakers of the BioExcel Virtual Workshop on Best Practices in QM/MM Simulation of Biomolecular Systems, who are:
Maria João Ramos (University of Porto)
Adrian Mulholland (University of Bristol)
Maria Khrenova (Lomonosov Moscow State University and Russian Academy of Sciences Research Centre “Fundamentals of Biotechnology”)
Ulf Ryde (Lund University)
Carme Rovira (University of Barcelona and Catalan Institute for Research and Advanced Studies)
Janez Mavri (Slovenia National Institute of Chemistry)
Emiliano Ippoliti (Forschungszentrum Jülich)
Dmitry Morozov (University of Jyväskylä)
Gerrit Groenhof (University of Jyväskylä)
- Overview and summary
- Detailed advice on individual topics
- How can QM/MM best be used in biomolecular research?
- Structure / model preparation and validation
- QM/MM modelling / simulation protocol and validation
- How best to choose a level of theory?
- How best to choose a suitable DFT functional?
- How best to choose a suitable QM region size?
- How best to choose the valence saturation scheme at the QM-MM boundary?
- Is the electrostatic coupling always the best compromise for the QM/MM coupling?
- What kind of systematic basis set benchmarking should one perform?
- How to choose a good collective variable (reaction coordinate) and perform effective sampling?
- Long-range electrostatics: truncate or not?
- Validation, analysis and interpretation of simulation results