MDAnalysis and Alchemical Simulations

This talk was recorded at the CCPBioSim Industry Talk on 19 June 2024. The speaker is Richard Gowers, one of the MDAnalysis developers.

Abstract: MDAnalysis is a popular Python package for the analysis of molecular dynamics simulation data. After introducing the package in broad strokes, this talk will give insight into how this package has been used and extended to process data coming from so-called “alchemical simulations”; where molecules are perturbed through non-physical states to provide estimates of properties such as binding affinities. Topics included will be biopolymer recognition, handling of multistate simulation data and analysing hybrid topology alchemical models.