MDAnalysis as a building block

While our documentation is mostly focused on using MDAnalysis for exploratory analysis it is equally well suited to build your own analysis library on top of it. Below is a list of all projects we know about that use MDAnalysis.

Visualization tools

1. nglview: nglview is a tool to visualize trajectories in jupyter notebooks.
2. mda-pymol: MDAnalysis has been embedded into PyMOL to read many different MD formats directly

Analysis tools

1. pydiffusion: Analyze the rotational diffusion of your molecules.
2. pytim: Pytim is a package based on MDAnalysis for the identification and analysis of surface molecules in configuration files or in trajectories from molecular dynamics simulations.
3. pycontact: Analysis of non-covalent interactions in MD trajectories.
4. pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data
5. RotamerConvolveMD: Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
6. PBxplore: PBxplore is a suite of tools dedicated to Protein Block (PB) analysis.
7. cgheliparm: Scripts used to analyze dsDNA structures from Martini MD simulations.
8. accelerated_sampling_with_autoencoder: This is the framework for running accelerated sampling with data-augmented autoencoders.

Distributions

MDAnalysis is also included in NMRBox a distribution of common software to analyze NMR measurements.

If you know of other tools that are build on MDAnalysis please share them with us on Twitter.