Examples

This page provides a series of examples, tutorials and recipes to help you get started with mdtraj.

Each subsection is a notebook. To open these notebooks in a “live” Jupyter/IPython session and execute the documentation interactively, you need to download the repository and start the Jupyter notebook.

If you installed MDTraj from source, you will need to navigate to path-to-mdtraj/examples. The notebook files for these examples and the notebooks are available in the top level examples folder on github too. In the directory with the notebook files, start an IPython notebook server:

$ jupyter notebook

Warning

The pre-filled out notebooks are far less fun than running them yourself!

• Introduction to MDTraj
• Atom Selection
• Finding centroids of clusters
• Clustering with md.rmsd() and scipy.cluster.hierarchy()
• Baker-Hubbard Hydrogen Bond Identification
• Out-of-core calculations with md.iterload()
• Fraction of Native Contacts
• Calculating NMR observables with mdtraj.nmr()
• Running a simulation in OpenMM
• Principal components analysis (PCA) with scikit-learn
• Plotting a Ramachandran map with matplotlib
• Benchmarking MDTraj’s RMSD engine
• Solvent Accessible Surface Area (SASA) Calculation
• Memory-limited two pass clustering with scipy.cluster

Let us know if you would like to contribute other example notebooks, or have any suggestions for how these can be improved.