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Simulation Analysis with MDTraj.

Introduction.

This tutorial provides a basic introduction to the use of iPython (Jupiter) notebooks for the interactive analysis of MD simulation data, leveraging the power of numpy for maths, matplotlib for plotting, and MDTraj for MD data analysis.

It consists of:

  1. An interactive iPython (Jupiter) notebook and associated data files.

It is available as a compressed tar file (c. 1.7 Mb) here.

Instructions.

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

  • numpy
  • scipy
  • cython
  • mdtraj
  • matplotlib
  • jupyter

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

Updated