Examples

MDAnalysis maintains a collection of Jupyter notebooks as examples of what the code can do. Each notebook can be downloaded from GitHub to run on your own computer, or viewed as an online tutorial on the user guide. You can also interact with each notebook on Binder.

General

• Quick start guide
• Constructing, modifying, and adding to a Universe
• Transformations
• Other

Analysis

• Alignments and RMS fitting
  • Aligning a structure to another
  • Aligning a trajectory to a reference
  • Aligning a trajectory to itself
  • Calculating the root mean square deviation of atomic structures
  • Calculating the pairwise RMSD of a trajectory
  • Calculating the root mean square fluctuation over a trajectory
• Distances and contacts
  • Atom-wise distances between matching AtomGroups
  • All distances between two selections
  • All distances within a selection
  • Fraction of native contacts over a trajectory
  • Q1 vs Q2 contact analysis
  • Contact analysis: number of contacts within a cutoff
  • Write your own native contacts analysis method
• Trajectory similarity
  • Comparing the geometric similarity of trajectories
  • Calculating the Harmonic Ensemble Similarity between ensembles
  • Calculating the Clustering Ensemble Similarity between ensembles
  • Calculating the Dimension Reduction Ensemble Similarity between ensembles
  • Evaluating convergence
• Structure
  • Elastic network analysis
  • Average radial distribution functions
  • Calculating the RDF atom-to-atom
  • Protein dihedral angle analysis
  • Helix analysis
• Dimension reduction
  • Principal component analysis of a trajectory
  • Non-linear dimension reduction to diffusion maps
• Polymers and membranes
  • Determining the persistence length of a polymer
  • Analysing pore dimensions with HOLE2
• Volumetric analyses
  • Computing mass and charge density on each axis
  • Calculating the solvent density around a protein