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    73 repositories

    • mdanalysis

      Public
      MDAnalysis is a Python library to analyze molecular dynamics simulations.
      pythonsciencemolecular-dynamicscomputational-chemistrymolecular-simulationmolecular-dynamics-simulationtrajectory-analysismdanalysis
      Python
      •
      Other
      •690•1.4k•428•63•Updated Mar 14, 2025Mar 14, 2025

    • MDAnalysis.github.io

      Public
      MDAnalysis home page mdanalysis.org as GitHub pages.
      CSS
      •43•14•16•11•Updated Mar 14, 2025Mar 14, 2025

    • benchmarks

      Public
      Performance benchmarks of MDAnalysis provided by ASV.
      mdanalysis
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Mar 13, 2025Mar 13, 2025

    • UserGuide

      Public
      User Guide for MDAnalysis
      Python
      •
      GNU Lesser General Public License v2.1
      •37•24•60•6•Updated Mar 12, 2025Mar 12, 2025

    • 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•1•Updated Mar 9, 2025Mar 9, 2025

    • MDAKits

      Public
      The MDAnalysis Toolkits Registry
      Python
      •
      Other
      •27•17•33•10•Updated Mar 9, 2025Mar 9, 2025

    • cookiecutter-mdakit

      Public
      Cookiecutter for Python packages based on MDAnalysis
      Python
      •
      MIT License
      •5•7•32•2•Updated Feb 23, 2025Feb 23, 2025

    • helanal

      Public
      A package to characterise the geometry of protein helicies.
      Python
      •1•0•0•1•Updated Feb 19, 2025Feb 19, 2025

    • mda-openbabel-converter

      Public
      MDAnalysis-OpenBabel Converter
      Python
      •
      Other
      •1•0•5•0•Updated Feb 18, 2025Feb 18, 2025

    • MDAnalysisWorkshop-Intro0.5Day

      Public
      Materials for 0.5-day MDAnalysis workshops
      Jupyter Notebook
      •
      Other
      •7•7•5•0•Updated Feb 10, 2025Feb 10, 2025

    • distopia

      Public
      SIMD instructions for faster distance calculations.
      C++
      •
      MIT License
      •6•12•9•1•Updated Feb 9, 2025Feb 9, 2025

    • mdanalysis-compatible-python

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 7, 2025Jan 7, 2025

    • imd-workshop-2024

      Public
      Materials for the virtual 2024 MDAnalysis IMD streaming workshop.
      pythonstreaminglammpsnamdgromacsmdanalysis
      Jupyter Notebook
      •1•7•0•0•Updated Dec 18, 2024Dec 18, 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•6•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•6•9•1•Updated Nov 25, 2024Nov 25, 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

    • 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-simulationgromacstrajectory
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •5•13•9•2•Updated Nov 11, 2024Nov 11, 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-managermdanalysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•15•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•4•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-analysismdanalysispython
      Python
      •
      GNU General Public License v3.0
      •7•31•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•11•19•2•Updated Aug 18, 2024Aug 18, 2024

    • omnireader

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