Projects in Awesome Lists by MDAnalysis
A curated list of projects in awesome lists by MDAnalysis .
https://github.com/mdanalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
computational-chemistry mdanalysis molecular-dynamics molecular-dynamics-simulation molecular-simulation python science trajectory-analysis
Last synced: 12 May 2025
https://github.com/mdanalysis/solvation-analysis
A comprehensive tool for analyzing liquid solvation structure.
Last synced: 11 Apr 2025
https://github.com/mdanalysis/panedr
Reads Gromacs EDR file to populate a pandas dataframe
Last synced: 06 Apr 2025
https://github.com/mdanalysis/pmda
Parallel algorithms for MDAnalysis
analysis dask mdanalysis molecular-dynamics parallel
Last synced: 12 Apr 2025
https://github.com/mdanalysis/membrane-curvature
MDAnalysis tool to calculate membrane curvature.
mdanalysis molecular-dynamics-simulation python trajectory-analysis
Last synced: 25 Apr 2026
https://github.com/mdanalysis/workshopprace2021
Materials for the 2021 PRACE Workshop @ SurfSARA
Last synced: 09 Apr 2025
https://github.com/mdanalysis/griddataformats
GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.
Last synced: 05 Apr 2025
https://github.com/mdanalysis/mdacli
Command line interface for MDAnalysis
cli command-line command-line-tool computational-chemistry mdanalysis molecular-dynamics molecular-dynamics-simulation python science trajectory-analysis
Last synced: 23 Jan 2026
https://github.com/mdanalysis/mdanalysisdata
Access to data for workshops and extended tests of MDAnalysis.
dataset-manager mdanalysis molecular-dynamics python
Last synced: 03 Apr 2026
https://github.com/mdanalysis/workshophackathon2018
Materials, issues and things for the 2018 Workshop and Hackathon
Last synced: 09 Apr 2025
https://github.com/mdanalysis/mdanalysis.github.io
MDAnalysis home page mdanalysis.org as GitHub pages.
Last synced: 10 Apr 2025
https://github.com/mdanalysis/transport-analysis
A Python package to compute and analyze transport properties.
Last synced: 26 Jun 2025
https://github.com/mdanalysis/pytng
Python bindings for TNG file format
file-format gromacs molecular-dynamics-simulation trajectory
Last synced: 24 Aug 2025
https://github.com/mdanalysis/distopia
SIMD instructions for faster distance calculations.
Last synced: 25 Aug 2025
https://github.com/mdanalysis/stride
STRIDE: Protein secondary structure assignment from atomic coordinates
Last synced: 09 Apr 2025
https://github.com/mdanalysis/rotamerconvolvemd
Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
deer electron-paramagnetic-resonance mdanalysis molecular-dynamics-simulation pre python science
Last synced: 09 Apr 2025
https://github.com/mdanalysis/imd-workshop-2024
Materials for the virtual 2024 MDAnalysis IMD streaming workshop.
gromacs lammps mdanalysis namd python streaming
Last synced: 12 Apr 2025
https://github.com/mdanalysis/cookiecutter-mdakit
Cookiecutter for Python packages based on MDAnalysis
Last synced: 13 Sep 2025
https://github.com/MDAnalysis/imd-workshop-2024
Materials for the virtual 2024 MDAnalysis IMD streaming workshop.
gromacs lammps mdanalysis namd python streaming
Last synced: 23 Apr 2025
https://github.com/mdanalysis/mdanalysisworkshop-intro0.5day
Materials for 0.5-day MDAnalysis workshops
Last synced: 30 Jun 2025
https://github.com/mdanalysis/mdahole2
An MDAKit implementing a Python interface for the HOLE program.
mdanalysis python structural-biology
Last synced: 09 Apr 2025
https://github.com/mdanalysis/waterdynamics
Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
Last synced: 09 Apr 2025
https://github.com/mdanalysis/binder-notebook
Notebooks for interactive use on https://mybinder.org/
binder jupyter-notebook mdanalysis notebook
Last synced: 09 Apr 2025
https://github.com/mdanalysis/mdalint
Proof of concept for a MDAnalysis linter
Last synced: 14 Mar 2026
https://github.com/mdanalysis/mdanalysisworkshop-intermediate1day
Materials for 1-day intermediate workshop
Last synced: 09 Apr 2025
https://github.com/mdanalysis/ugm2023
Materials for the 2023 MDAnalysis User Group Meeting
Last synced: 09 Apr 2025
https://github.com/mdanalysis/ugm2025
Materials for the 2025 MDAnalysis User Group Meeting
Last synced: 18 Feb 2026
https://github.com/mdanalysis/rdkitconverter-benchmark
Benchmark for the RDKitConverter's inferring of bond orders and charges
Last synced: 23 Jan 2026
https://github.com/mdanalysis/mdakits-whitepaper
MDAKits whitepaper (LaTeX sources).
mdanalysis overleaf-sync publication
Last synced: 24 Jan 2026
https://github.com/mdanalysis/benchmarks
Performance benchmarks of MDAnalysis provided by ASV.
Last synced: 09 Apr 2025
https://github.com/mdanalysis/mdanalysissandbox
testing reporsitory for workshops
Last synced: 26 Jun 2025
https://github.com/mdanalysis/scipy-2016
Accepted proposal for a talk at SciPy 2016
Last synced: 19 Mar 2026
https://github.com/mdanalysis/helanal
A package to characterise the geometry of protein helicies.
Last synced: 11 Sep 2025
https://github.com/mdanalysis/mdanalysis-sphinx-theme
The official MDAnalysis Sphinx documentation theme.
Last synced: 09 Apr 2025
https://github.com/mdanalysis/mda-xdrlib
Stand-alone XDRLIB module (from cpython 3.10.8)
Last synced: 20 Aug 2025
https://github.com/mdanalysis/ugm2024
Materials for the 2024 MDAnalysis User Group Meeting
Last synced: 09 Apr 2025
https://github.com/mdanalysis/mdanalysisworkshop-intro1day
Materials for 1-day MDAnalysis workshops
Last synced: 14 May 2025
https://github.com/mdanalysis/spidal-mdanalysis-midas-tutorial
Tutorial for SPIDAL presentation at workshop, showing how to use Midas radical.pilot to analyze an ensemble of MD trajectories with Path Similarity Analysis (as implemented in MDAnalysis).
mdanalysis python science spidal tutorial
Last synced: 14 May 2025
https://github.com/mdanalysis/binder-env-userguide
Binder environment of the User Guide
Last synced: 13 Feb 2026
https://github.com/mdanalysis/pathsimanalysis
An MDAKit that calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff or Fréchet distances.
Last synced: 05 Jan 2026
https://github.com/mdanalysis/mdgeomkit
Simple cookie-cutter based MDAKit (for Workshop teaching)
Last synced: 03 Jan 2026
https://github.com/mdanalysis/pypi-deployment
Reusable github action to package, deploy and and check code to PyPi & TestPyPi
Last synced: 27 Feb 2026
https://github.com/mdanalysis/mdaencore
Ensemble overlap comparison software for molecular data.
Last synced: 30 Jan 2026
https://github.com/mdanalysis/install-mdanalysis
Action to install MDAnalysis
Last synced: 25 Jan 2026