This workshop illustrates the application of a number of Python-based tools to the analysis of the results from a short (1 nanosecond) simulation of ubiquitin, investigating the question "how similar is the MD trajectory to the crystal and NMR structures?"
The workshop illustrates:
- The use of the Python MDTraj module (see http://www.mdtraj.org)
- The use of the Python matplotlib module for plotting (see http://www.matplotlib.org)
- The use of the Python MDPlus module for Principal Component Analysis (see http://bitbucket.org/claughton/mdplus)