Used By

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 projects we know about that use MDAnalysis.

If you know of other tools that use MDAnalysis please share them with us on Twitter or on our mailinglist so that we can include them here or open a pull request by editing the file used-by.md.

Visualization tools

• nglview: nglview is a tool to visualize trajectories in jupyter notebooks.
• MDSrv streams and visualizes MD trajectories interactively within web browsers
• mda-pymol: MDAnalysis has been embedded into PyMOL to read many different MD formats directly (see bieniekmateusz/pymol-mdanalysis on GitHub)
• MolecularNodes plugin for the Blender rendering package; the plugin provides a convenient method for importing structural biology files, including MD trajectories, into Blender, and several nodes for working with atomic data inside of Blender’s Geometry Nodes.

Analysis tools

• pydiffusion: Analyze the rotational diffusion of your molecules.
• 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.
• pycontact: Analysis of non-covalent interactions in MD trajectories.
• RotamerConvolveMD: Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
• PBxplore: PBxplore is a suite of tools dedicated to Protein Block (PB) analysis.
• cgheliparm: Scripts used to analyze dsDNA structures from Martini MD simulations.
• accelerated_sampling_with_autoencoder: This is the framework for running accelerated sampling with data-augmented autoencoders.
• BioEn: BioEn integrates a broad range of experimental data to refine ensembles of structures.
• kugupu: A molecular network generator to study charge transport pathways in amorphous materials
• PyInteraph: A software tool for the analysis of structural communication in protein ensembles, including a PyMOL plugin and an InteractionPlotter.
• MAICoS: Analyze molecular dynamics simulations of interfacial and confined systems.
• taurenmd: A command-line interface for analysis of Molecular Dynamics simulations.
• PENSA: A toolkit for exploratory analysis and comparison of protein structural ensembles
• LiPyphilic: A Python package for the analysis of lipid membrane simulations.
• MDVoxelSegmentation: A voxel-based approach for dynamic cluster analysis of molecular dynamics trajectories.

Molecular modeling tools

• Swarm-CG: Automatically optimizes the bonded terms of a MARTINI-like coarse-grained (CG) molecular model with respect to its reference all-atom (AA) trajectory, via FST-PSO.

Simulation packages

• ESPResSo is a software package for performing and analyzing Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology.

Distributions

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

Some generic distributions such as MacPorts: py-MDAnalysis (macOS), Fedora: python-MDAnalysis and archlinux: python-mdanalysis (Linux) maintain packages of MDAnalysis.