A Python toolkit for analysing molecular dynamics simulations.

MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists.

The goal of MDAnalysis is to make it easy for users to analyze data that are produced by simulations (primarily molecular dynamics (MD) simulations) that run on some of the largest supercomputers in the world. MDAnalysis accomplishes this goal by providing a toolkit of programming building blocks that provide an abstract Python interface to the simulation data — agnostic of the specific simulation package that produced it — that lends itself to interactive data exploration and rapid prototyping but is also a robust foundational library that can form the basis for new computational tools.

MDAnalysis allows one to read particle-based trajectories such as the ones produced by MD simulations or individual coordinate frames (such as biomolecules in the protein databank (PDB) format) and access the atomic coordinates through NumPy arrays. Together with a powerful selection language and many implemented analysis algorithms, MDAnalysis provides a flexible and fast framework for complex analysis tasks.

MDAnalysis is a project written by scientists for scientists and is used for cutting edge research in biophysics, chemistry, softmatter physics, and materials research around the world in academia and national research labs. MDAnalysis strives to be highly interoperable and hence a growing number of projects use MDAnalysis as their foundational library or integrate it. Welcoming documentation such as the new User Guide make it easy to get started. New releases are downloaded a few thousand times and the academic papers describing MDAnalysis are cited almost a thousand times, indicating the widespread use in the academic community.

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Technologies

  • python
  • cython
  • numpy
  • c/c++

Topics

  • Science and Medicine
  • biophysics
  • computational chemistry
  • molecular simulation
  • cheminformatics
  • molecular dynamics
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MDAnalysis 2020 Projects

  • Cédric Bouysset
    From RDKit to the Universe and back
    The aim of the RDKit interoperability project is to give MDAnalysis the ability to use RDKit’s Chem.Mol structure as an input to an MDAnalysis’...
  • Yuxuan Zhuang
    Serialize Universes for parallel
    MDAnalysis is a flexible and relatively fast framework for complex analysis tasks in molecular dynamics (MD) simulations. To achieve a flawless...
  • Hugo MacDermott-Opeskin
    Trajectory New Generation: the trajectory format for the future of simulation
    Trajectory storage has always proved problematic for the molecular simulation community, as large volumes of data can be generated quickly....
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2020