Special Seminar: Crimes against Chemistry and how to avoid them!

Talk by Sarah Harris (University of Leeds) recorded at the CCPBioSim Training Week 2021.

Chemistry is at the very centre of every biomolecular simulation, because it determines how your biomolecule is constructed in the computer model. Unless you have a grasp of how your simulation represents chemical interactions, you may find it difficult to debug issues with your simulation setup or your trajectories. Here I will describe the most common problems and pitfalls that non-chemists face when performing biomolecular simulations, and how to solve them. I will show how to use visualisation tools to check simulation setup and results, and how chemical insight can be used to analyse trajectories, such as understanding the role of hydrogen bonds or hydrophobic stacking interactions. I will also advise on research questions that are best avoided by teams that do not include strong chemistry expertise.