Repositories list

• MartiniSurf

  Public
  MartiniSurf: a package for the preparation of Martini simulations of immobilized proteins

  Python

  •

  MIT License

  •0•1•3•0•Updated Mar 27, 2026Mar 27, 2026

• MasterMSM

  Public
  Python package for generating Markov state models

  molecular-dynamicsmarkov-state-modelprotein-folding

  molecular-dynamicsmarkov-state-modelprotein-folding

  Python

  •

  GNU General Public License v2.0

  •7•17•0•1•Updated Mar 13, 2026Mar 13, 2026

• Stickers

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• NCIfolding

  Public
  Python

  •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• lj-openmm

  Public
  Lennard Jones simulation using OpenMM

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• PLUMED-docs

  Public
  Working examples of different types of molecular dynamics simulations that can be run using Gromacs patched with PLUMED

  Jupyter Notebook

  •0•1•0•0•Updated Jan 8, 2025Jan 8, 2025

• CALVADOS

  Public
  Python

  •

  GNU General Public License v3.0

  •23•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• rest2_tests

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 11, 2024Mar 11, 2024

• ResDocs

  Public
  HTML

  •0•0•0•0•Updated Aug 29, 2023Aug 29, 2023

• AdaptiveMasterMSM

  Public
  Adaptive sampling implementation interacting with MasterMSM

  Python

  •

  GNU General Public License v2.0

  •2•3•0•0•Updated Mar 24, 2022Mar 24, 2022

• hdbMSM

  Public
  Contains notebooks used to carry out all the calculations related to the paper Markov state models from hierarchical density based assignment

  Jupyter Notebook

  •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022