This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
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 training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/pca-workshop:latest
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/ccpbiosim/pca-workshop:latest
Workshop Content Authors:
- Charlie Laughton
Please direct all questions and feedback to Charlie Laughton