The aim of the workshop is to illustrate methods we can use to assess convergence and sampling in MD trajectories. You will compare and contrast the most basic and widely-used method to do this - RMSD analysis - with the use of more sophisticated approaches based on Principal Component Analysis (PCA).
You will apply the approaches to two common scenarios: firstly the comparison of the dynamics of a protein the presence and absence of a bound ligand, and secondly the evaluation of sampling and convergence in an ensemble of independent, replicate, MD trajectories of a protein.
A basic knowledge of Python and MD analysis methods.
A Jupyter notebook and associated data files.
Please direct all comments and enquiries to Charlie Laughton
