Repositories list

• benchmarks

  Public
  Performance benchmarks of MDAnalysis provided by ASV.

  mdanalysis

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•0•0•Updated Dec 28, 2024Dec 28, 2024

• mdanalysis

  Public
  MDAnalysis is a Python library to analyze molecular dynamics simulations.

  pythonsciencemolecular-dynamics+ 5computational-chemistrymolecular-simulationmolecular-dynamics-simulationtrajectory-analysismdanalysis

  Python

  •

  Other

  •660•1.3k•431•61•Updated Dec 28, 2024Dec 28, 2024

• UserGuide

  Public
  User Guide for MDAnalysis

  Python

  •

  GNU Lesser General Public License v2.1

  •37•23•55•4•Updated Dec 27, 2024Dec 27, 2024

• MDAKits

  Public
  The MDAnalysis Toolkits Registry

  Python

  •

  Other

  •26•17•33•9•Updated Dec 22, 2024Dec 22, 2024

• imd-workshop-2024

  Public
  Materials for the virtual 2024 MDAnalysis IMD streaming workshop.

  pythonstreaminglammps+ 3namdgromacsmdanalysis

  Jupyter Notebook

  •1•5•0•0•Updated Dec 18, 2024Dec 18, 2024

• MDAnalysis.github.io

  Public
  MDAnalysis home page mdanalysis.org as GitHub pages.

  CSS

  •41•14•23•2•Updated Dec 12, 2024Dec 12, 2024

• distopia

  Public
  SIMD instructions for faster distance calculations.

  C++

  •

  MIT License

  •6•10•13•1•Updated Dec 3, 2024Dec 3, 2024

• cookiecutter-mdakit

  Public
  Cookiecutter for Python packages based on MDAnalysis

  Python

  •

  MIT License

  •5•7•32•2•Updated Dec 1, 2024Dec 1, 2024

• waterdynamics

  Public
  Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.

  Python

  •

  GNU Lesser General Public License v2.1

  •4•5•9•2•Updated Nov 25, 2024Nov 25, 2024

• mdahole2

  Public
  An MDAKit implementing a Python interface for the HOLE program.

  pythonstructural-biologymdanalysis

  Python

  •

  GNU Lesser General Public License v2.1

  •3•5•9•1•Updated Nov 25, 2024Nov 25, 2024

• PathSimAnalysis

  Public
  An MDAKit that calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff or Fréchet distances.

  Python

  •

  GNU Lesser General Public License v2.1

  •1•0•3•2•Updated Nov 23, 2024Nov 23, 2024

• pypi-deployment

  Public
  Reusable github action to package, deploy and and check code to PyPi & TestPyPi

  MIT License

  •0•0•2•0•Updated Nov 23, 2024Nov 23, 2024

• mdanalysis-sphinx-theme

  Public
  The official MDAnalysis Sphinx documentation theme.

  Sass

  •

  Other

  •1•1•6•4•Updated Nov 12, 2024Nov 12, 2024

• GridDataFormats

  Public
  GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.

  python

  Python

  •

  GNU Lesser General Public License v3.0

  •18•29•6•1•Updated Nov 11, 2024Nov 11, 2024

• helanal

  Public
  A package to characterise the geometry of protein helicies.

  Python

  •1•0•0•1•Updated Nov 11, 2024Nov 11, 2024

• panedr

  Public
  Reads Gromacs EDR file to populate a pandas dataframe

  Python

  •

  GNU Lesser General Public License v2.1

  •7•31•2•0•Updated Nov 11, 2024Nov 11, 2024

• mdaencore

  Public
  Ensemble overlap comparison software for molecular data.

  Python

  •

  GNU General Public License v2.0

  •0•0•19•1•Updated Nov 11, 2024Nov 11, 2024

• pytng

  Public
  Python bindings for TNG file format

  file-formatmolecular-dynamics-simulationgromacs+ 1trajectory

  C

  •

  BSD 3-Clause "New" or "Revised" License

  •5•13•9•2•Updated Nov 11, 2024Nov 11, 2024

• mda-openbabel-converter

  Public
  MDAnalysis-OpenBabel Converter

  Python

  •

  MIT License

  •1•0•9•0•Updated Oct 25, 2024Oct 25, 2024

• mdanalysis-compatible-python

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 21, 2024Oct 21, 2024

• branding

  Public
  Resources for MDAnalysis branding

  1•0•0•0•Updated Oct 5, 2024Oct 5, 2024

• MDAnalysisData

  Public
  Access to data for workshops and extended tests of MDAnalysis.

  pythonmolecular-dynamicsdataset-manager+ 1mdanalysis

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•14•7•2•Updated Sep 25, 2024Sep 25, 2024

• mda-xdrlib

  Public
  Stand-alone XDRLIB module (from cpython 3.10.8)

  Python

  •

  Other

  •0•1•1•0•Updated Sep 19, 2024Sep 19, 2024

• UGM2024

  Public
  Materials for the 2024 MDAnalysis User Group Meeting

  Jupyter Notebook

  •

  Other

  •2•1•0•0•Updated Sep 6, 2024Sep 6, 2024

• MDAnalysisWorkshop-Intermediate1Day

  Public
  Materials for 1-day intermediate workshop

  Jupyter Notebook

  •

  Other

  •1•3•1•0•Updated Sep 5, 2024Sep 5, 2024

• mdakit-cookie

  Public
  0•0•0•0•Updated Sep 1, 2024Sep 1, 2024

• membrane-curvature

  Public
  MDAnalysis tool to calculate membrane curvature.

  molecular-dynamics-simulationtrajectory-analysismdanalysis+ 1python

  Python

  •

  GNU General Public License v3.0

  •7•30•5•1•Updated Aug 20, 2024Aug 20, 2024

• transport-analysis

  Public
  A Python package to compute and analyze transport properties.

  Python

  •

  GNU General Public License v2.0

  •2•10•19•2•Updated Aug 18, 2024Aug 18, 2024

• omnireader

  Public
  Cython

  •0•0•3•2•Updated Aug 16, 2024Aug 16, 2024

• RDKitConverter-benchmark

  Public
  Benchmark for the RDKitConverter's inferring of bond orders and charges

  HTML

  •

  GNU General Public License v2.0

  •0•3•2•0•Updated Aug 7, 2024Aug 7, 2024