Projects in Awesome Lists tagged with 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/chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit

Last synced: 20 Nov 2025

https://github.com/AngelRuizMoreno/Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit

Last synced: 22 Jul 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/pmda

Parallel algorithms for MDAnalysis

analysis dask mdanalysis molecular-dynamics parallel

Last synced: 12 Apr 2025

https://github.com/mdanalysis/workshopprace2021

Materials for the 2021 PRACE Workshop @ SurfSARA

mdanalysis

Last synced: 09 Apr 2025

https://github.com/becksteinlab/propkatraj

pKa estimates for proteins using an ensemble approach

mdanalysis molecular-dynamics-simulation pandas pka-predictions

Last synced: 03 Apr 2025

https://github.com/bio-phys/pydiffusion

Analyse Rotational Diffusion Tensor from MD Simulations

brownian-dynamics diffusion mdanalysis molecular-dynamics python rotation simulation

Last synced: 16 Jan 2026

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/yuxuanzhuang/ggmolvis

Molecular visualization for MDAnalysis with MolecularNodes in Blender

blender mdanalysis molecular-dynamics molecularnodes visualization

Last synced: 09 Apr 2025

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/becksteinlab/hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

mdanalysis molecular-dynamics python science solvation water

Last synced: 28 Feb 2026

https://github.com/becksteinlab/zarrtraj

zarrtraj MDAKit for @MDAnalysis

file-format mdanalysis molecular-dynamics streaming zarr

Last synced: 23 Apr 2025

https://github.com/becksteinlab/imdclient

Streaming analysis from running MD simulations.

md mdanalysis python science streaming

Last synced: 14 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: 23 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/mdahole2

An MDAKit implementing a Python interface for the HOLE program.

mdanalysis python structural-biology

Last synced: 09 Apr 2025

https://github.com/becksteinlab/mdanalysis-with-dask

Benchmarking MDAnalysis with dask.

dask hpc mdanalysis molecular-dynamics-simulation mpi python spidal

Last synced: 18 Jul 2025

https://github.com/simongravelle/mdanalysis-tutorial

Perform post-mortem analysis using Python and MDAnalysis

guide lammps mdanalysis molecular-dynamics tutorial

Last synced: 06 Sep 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/becksteinlab/parallel-analysis-in-the-mdanalysis-library

Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.

benchmark dask mdanalysis mpi trajectory

Last synced: 23 Apr 2025

https://github.com/mdanalysis/benchmarks

Performance benchmarks of MDAnalysis provided by ASV.

mdanalysis

Last synced: 09 Apr 2025

https://github.com/mdanalysis/mdakits-whitepaper

MDAKits whitepaper (LaTeX sources).

mdanalysis overleaf-sync publication

Last synced: 24 Jan 2026

https://github.com/becksteinlab/imdreader

prototype IMDReader for MDAnalysis

md mdanalysis streaming

Last synced: 31 Oct 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