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Analysis of MD Trajectories

Requirements:

Basic knowledge of the Linux command line.

Training Material

This workshop consists of a series of Jupyter notebooks:

  1. Basic Analysis: An introduction to interactive MD data analysis with Jupyter notebooks and MDTraj.
  2. PCA Analysis: An introduction to the use of Principal Component Analysis methods for the analysis of sampling and convergence of MD simulations.
  3. Statistical Analysis: An introduction to the use of statistical methods to assess the significance of data extracted from MD simulations.
  4. Ubiquitin Analysis: Application of some of the methods in the other notebooks to the analysis of data from an MD simulation of ubiquitin.
  5. Prokpka Analysis: Analysis of a PDB structure using Propka to predict protonation states of acidic and basic residues.
  6. Procheck Analysis: A slightly more advanced notebook that demonstartes how you can automate the Procheck analysis of a multi-model PDB file of an NMR-derived protein structure.

These can be run using the CCPBioSim workshop server. Once you have started the server, navigate to the md_workshop directory and you will find the notebooks there.

If you want to take a copy for your own use back home, the simplest approach is to clone this repository:

git clone https://github.com/CCPBioSim/md_workshop.git