QM/MM Best Practice Workshop: Kick-off webinar
Channel: BioExcel CoE
Date: 04/11/2020

Gerrit Groenhof presents the first 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.4264626

Multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) simulations have become a popular method for obtaining mechanistic insights into a variety of biomolecular research areas. However QM/MM techniques rely on approximations such as the size of the QM region, the level of QM theory and the MM description. In order to increase confidence in results from QM/MM simulations these approximations require careful validation prior to simulation. With the exception perhaps of ultrafast photo-induced processes, chemical reaction timescales preclude an unbiased sampling of all available reaction pathways. For this reason, QM/MM calculations are typically combined with enhanced sampling techniques, often along predefined reaction coordinates. In addition to considering the accuracy of the QM/MM model, the sampling techniques involved therefore also require validation for the problem at hand.

Consider enzymes for example – an important component in biotechnology. To systematically improve enzymes for biotechnological applications, a detailed understanding of the underlying reaction mechanism is needed. As the time and spatial resolution required to gain atomistic insights into enzymatic activity have been essentially impossible to achieve experimentally (at least until very recently), most of our current knowledge is based on either inference from extensive experimentation or from computer simulations.

In this first QM/MM Best Practice Workshop webinar Gerrit Groenhof discusses and illustrate these tricky but essential aspects of performing QM/MM simulation in the context of his and his collaborators' work on biological photoreceptors and on ATP hydrolysis in an ABC transporter.


References: see https://bioexcel.eu/qm-mm-best-practice-workshop-kick-off-webinar-2020-10-30/