Repositories list

• adaptivemd

  Public archive
  A python framework to run adaptive Markov state model (MSM) simulation on HPC resources

  pythonmarkov-modelhpc+ 2

  pythonmarkov-modelhpcmolecular-dynamics-simulationadaptive

  Python

  •

  GNU Lesser General Public License v2.1

  •88 forks•1717 stars•1717 issues•22 pull requests•Updated Aug 1, 2025Aug 1, 2025

• mdshare

  Public
  Get access to our MD data files.

  trajectories

  trajectories

  Python

  •

  GNU Lesser General Public License v3.0

  •66 forks•3434 stars•44 issues•11 pull request•Updated Nov 22, 2023Nov 22, 2023

• PyEMMA

  Public archive
  🚂 Python API for Emma's Markov Model Algorithms 🚂

  pythonmarkov-modelhmm+ 11

  pythonmarkov-modelhmmtime-seriesanalysismolecular-dynamicsbayesian-methodsticahidden-markov-modelmarkov-state-model+ 4

  Python

  •

  GNU Lesser General Public License v3.0

  •129129 forks•340340 stars•5757 issues•00 pull requests•Updated Sep 11, 2023Sep 11, 2023

• ivampnets

  Public
  Python

  •22 forks•2525 stars•11 issue•00 pull requests•Updated Feb 28, 2023Feb 28, 2023

• msmtools

  Public
  Tools for estimating and analyzing Markov state models

  markov-modelanalysismarkov-state-model

  markov-modelanalysismarkov-state-model

  Python

  •

  GNU Lesser General Public License v3.0

  •2626 forks•4141 stars•00 issues•00 pull requests•Updated Aug 15, 2022Aug 15, 2022

• pyemma-workshop

  Public
  workshop-materialspyemma

  workshop-materialspyemma

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •88 forks•3232 stars•22 issues•00 pull requests•Updated Feb 24, 2022Feb 24, 2022

• decomposed_msms

  Public
  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 14, 2022Feb 14, 2022

• deepmsm

  Public
  Code to reproduce results for the paper: Progress in deep Markov State Modeling: Coarse graining and experimental data restraints

  Jupyter Notebook

  •33 forks•88 stars•00 issues•00 pull requests•Updated Oct 19, 2021Oct 19, 2021

• msmrd2

  Public
  C++

  •11 fork•55 stars•00 issues•00 pull requests•Updated Mar 18, 2021Mar 18, 2021

• PyEMMA_IPython

  Public
  PyEMMA Jupyter Notebooks

  pyemma

  pyemma

  Jupyter Notebook

  •1313 forks•1313 stars•22 issues•00 pull requests•Updated Jan 28, 2021Jan 28, 2021

• PySFD

  Public
  visualizationmolecular-dynamicsensemble+ 2

  visualizationmolecular-dynamicsensembleorder-parameterscollective-variables

  Python

  •

  GNU Lesser General Public License v3.0

  •66 forks•55 stars•00 issues•00 pull requests•Updated Jun 18, 2020Jun 18, 2020

• deep_rev_msm

  Public
  Jupyter Notebook

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 21, 2020Jan 21, 2020

• pyemma_tutorials

  Public
  How to analyze molecular dynamics data with PyEMMA

  markov-modeltutorialanalysis+ 4

  markov-modeltutorialanalysismolecular-dynamicskineticsmd-simulationspyemma

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •3434 forks•8888 stars•33 issues•00 pull requests•Updated May 29, 2019May 29, 2019

• deeptime

  Public
  Deep learning meets molecular dynamics.

  pythonmarkov-modelmachine-learning+ 9

  pythonmarkov-modelmachine-learningdeep-learningtime-seriestensorflowcomputational-biologypytorchcomputational-chemistryautoencoder+ 2

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •4040 forks•189189 stars•55 issues•00 pull requests•Updated May 3, 2019May 3, 2019

• molPX

  Public
  IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

  visualizationwidgetjupyter-notebook+ 4

  visualizationwidgetjupyter-notebookmolecular-dynamicsipython-notebookticafree-energy

  Python

  •

  GNU Lesser General Public License v3.0

  •44 forks•4343 stars•1212 issues•11 pull request•Updated Feb 14, 2019Feb 14, 2019

• compsci-2018

  Public
  Repository for the computational sciences software project of 2018/2019

  Jupyter Notebook

  •1212 forks•44 stars•33 issues•55 pull requests•Updated Feb 7, 2019Feb 7, 2019

• thermotools

  Public
  Winter is coming...

  Python

  •

  GNU Lesser General Public License v3.0

  •55 forks•1414 stars•00 issues•00 pull requests•Updated Jan 23, 2019Jan 23, 2019

• graphtime

  Public
  Encoding of transition probabilities with undirected graphical models

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •55 forks•99 stars•00 issues•00 pull requests•Updated Dec 14, 2018Dec 14, 2018

• feature_selection

  Public
  Variational approach to feature selection

  msmvampvamp-scores

  msmvampvamp-scores

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 27, 2018Nov 27, 2018

• deep_gen_msm

  Public
  Code for the results of the paper at https://arxiv.org/abs/1805.07601

  Jupyter Notebook

  •22 forks•55 stars•00 issues•00 pull requests•Updated Sep 10, 2018Sep 10, 2018

• msmrd

  Public
  MSMs coupled with reaction-diffusion dynamics

  Jupyter Notebook

  •11 fork•33 stars•00 issues•00 pull requests•Updated Aug 9, 2018Aug 9, 2018

• compsci-2017

  Public archive
  Repository for the computational sciences software project of 2017/2018

  Jupyter Notebook

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2018Jan 23, 2018

• compsci-2016

  Public archive
  Repository for the computational sciences project of 2016/2017

  Jupyter Notebook

  •77 forks•11 star•00 issues•00 pull requests•Updated Dec 19, 2016Dec 19, 2016

• variational

  Public archive
  Basis sets, estimators and solvers for the variational approach of conformation dynamics. NOTE: the code has been merged with PyEMMA and is maintained there.

  Python

  •55 forks•1010 stars•22 issues•00 pull requests•Updated Dec 8, 2016Dec 8, 2016

• msm-theory-sandbox

  Public
  A playground for examples and tools to explore the theory of MSMs and related models.

  Python

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Oct 18, 2016Oct 18, 2016

• basissets

  Public
  Basis sets for variational approach for conformational dynamics (VAC)

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2016Sep 22, 2016

• coordinates

  Public archive
  Python

  •00 forks•22 stars•1010 issues•00 pull requests•Updated Sep 16, 2016Sep 16, 2016

• mcmm-project

  Public archive
  Jupyter Notebook

  •99 forks•00 stars•00 issues•00 pull requests•Updated Jun 30, 2016Jun 30, 2016

• pytram

  Public archive
  The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA

  Python

  •22 forks•1010 stars•1212 issues•00 pull requests•Updated May 25, 2016May 25, 2016

• oom

  Public
  Code for observable operator models

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2015Aug 6, 2015