Aimed at: People with an interest in running free energy calculations
Requirements: Basic Python, Jupyter, BioSimSpace knowledge
Abstract: Alchemical free energy calculations can be used to efficiently compute binding free energies between a ligand and a protein or hydration free energies of a small molecule. In the last few years, the use of such methods has gained momentum not only within academia but also within the pharmaceutical industry. In order to run alchemical free energy simulations, a series of molecular dynamics simulations need to be carried out. The first part of this workshop will look at setting up and running binding free energy calculations with BioSimSpace, whereas the second part will introduce best practices for their analysis. As part of the analysis, we will cover thermodynamic integration, MBAR, as well as how to choose good simulation overlap using metrics from an overlap matrices.