The Analysis of MD Simulation Data.

Introduction.

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.

It is based on a tutorial given originally at the CCP-BioSim training workshop in September 2016.

It consists of:

1. An short introductory Powerpoint presentation.
2. An interactive iPython (Jupiter) notebook and associated data files.

It is available as a compressed tar file (c. 330 Mb) here.

Instructions.

You need a Python environment (>= 2.7) with the following packages installed:

• numpy
• scipy
• cython
• mdanalysis
• pyPcazip
• matplotlib
• jupyter

Then if you download and unpack the compressed tarball (see above), you should be ready to go.