QM/MM Best Practice: Obtaining accurate structures and energies with QM/MM
Channel: BioExcel CoE
Date: 26/11/2020

Ulf Ryde presents the third webinar in the BioExcel virtual workshop on Best Practices in QM/MM Simulation of Biomolecular Systems: https://bioexcel.eu/qmmm-best-practice-workshop
Slides: http://doi.org/10.5281/zenodo.4293910

In this webinar, Prof. Ulf Ryde discusses his approach to performing QM/MM calculations, emphasizing three aspects of QM/MM calculations developed in his group. The first is the combination of QM/MM calculations with experimental raw data in the form of X-ray or neutron crystallography, NMR or EXAFS measurements [3–6]. This has turned out to be a powerful approach to improve structures, determine what is really seen in the structures and settle protonation and oxidation states [7–10]. The second is the bigQM approach, in which we try to converge the energies with respect to the size of the QM system by performing single-point energy calculations including all residues within 4.5–6 Å of a minimal QM system, all buried charges in the protein and moving cut bonds at least three residues away from the active site, in total typically ~1000 atoms [11, 12]. The third is to calculate QM/MM free energies without actually performing QM/MM molecular dynamics simulations with the reference-potential approach [13, 14].

References: see https://bioexcel.eu/qmmm-best-practice-workshop-3