Welcome

This site hosts a selection of training material related to Biomolecular Simulation.

1. An Introduction to Simulation Analysis with MDTraj. This tutorial provides an introduction to interactive MD simulation analysis using iPython (Jupiter) notebooks, with numpy, matplotlib and MDTraj.

2. The Analysis of MD Simulation Data. This tutorial provides a basic introduction to methods for the evaluation of sampling and convergence in MD simulations. In particular, methods based on RMSD analysis are compared with those that use PCA.