Tutorial Jupyter Notebooks

@orbeckst gave an introductory presentation (available in PDF or Keynote08 format) on MDAnalysis, its philopsophy and overall structure and development process.

The workshop session was held by @dotsdl and @orbeckst. They live-coded in Jupyter notebooks.

Fundamentals

The notebook MDAnalysis_Workshop_Part_1.ipynb introduces the fundamental objects of MDAnalysis: the Universe, AtomGroup, and Atom objects. It also introduces the selection language, and the basics of reading and slicing trajectories.

Trajectory analysis

The notebook MDAnalysis_Workshop_Part_2.ipynb teaches how to work with trajectories. The lesson includes different ways to access and select frames and introduces common programming patterns for frame-based analysis, including a range of real-world examples using the trajectories from the Data Download section.

See also

• Have a look at the official MDAnalysis Tutorial.
• See the list of other tutorials.
• Join the discussion on the mdnalysis-discussion mailing list.