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.
This container is derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container. The source content for this course can be found at https://github.com/CCPBioSim/pca-workshop
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/jimboid/biosim-pca-workshop:latest
Please direct all comments and enquiries to Charlie Laughton