Repositories list

• adaptivemd

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

  pythonmarkov-modelhpc+ 2molecular-dynamics-simulationadaptive

  Python

  •

  GNU Lesser General Public License v2.1

  •8•18•17•3•Updated Apr 8, 2024Apr 8, 2024

• mdshare

  Public
  Get access to our MD data files.

  trajectories

  Python

  •

  GNU Lesser General Public License v3.0

  •5•25•3•1•Updated Nov 22, 2023Nov 22, 2023

• PyEMMA

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

  markov-modelhmmtime-series+ 11analysismolecular-dynamicsbayesian-methodsticahidden-markov-modelmarkov-state-modelumbrella-sampling+ 4

  Python

  •

  GNU Lesser General Public License v3.0

  •119•310•57•0•Updated Sep 11, 2023Sep 11, 2023

• ivampnets

  Public
  Python

  •2•24•1•0•Updated Feb 28, 2023Feb 28, 2023

• msmtools

  Public
  Tools for estimating and analyzing Markov state models

  markov-modelanalysismarkov-state-model

  Python

  •

  GNU Lesser General Public License v3.0

  •27•40•0•0•Updated Aug 15, 2022Aug 15, 2022

• pyemma-workshop

  Public
  workshop-materialspyemma

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •9•27•2•0•Updated Feb 24, 2022Feb 24, 2022

• decomposed_msms

  Public
  Jupyter Notebook

  •0•1•0•0•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

  •2•7•0•0•Updated Oct 19, 2021Oct 19, 2021

• msmrd2

  Public
  C++

  •1•3•0•0•Updated Mar 18, 2021Mar 18, 2021

• PyEMMA_IPython

  Public
  PyEMMA Jupyter Notebooks

  pyemma

  Jupyter Notebook

  •12•11•2•0•Updated Jan 28, 2021Jan 28, 2021

• PySFD

  Public
  visualizationmolecular-dynamicsensemble+ 2order-parameterscollective-variables

  Python

  •

  GNU Lesser General Public License v3.0

  •6•5•0•0•Updated Jun 18, 2020Jun 18, 2020

• deep_rev_msm

  Public
  Jupyter Notebook

  •1•2•0•0•Updated Jan 21, 2020Jan 21, 2020

• pyemma_tutorials

  Public
  How to analyze molecular dynamics data with PyEMMA

  markov-modeltutorialanalysis+ 4molecular-dynamicskineticsmd-simulationspyemma

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •35•72•3•0•Updated May 29, 2019May 29, 2019

• deeptime

  Public
  Deep learning meets molecular dynamics.

  pythonmarkov-modelmachine-learning+ 9deep-learningtime-seriestensorflowcomputational-biologypytorchcomputational-chemistryautoencoder+ 2

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •39•175•5•0•Updated May 3, 2019May 3, 2019

• molPX

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

  visualizationwidgetjupyter-notebook+ 4molecular-dynamicsipython-notebookticafree-energy

  Python

  •

  GNU Lesser General Public License v3.0

  •2•39•11•1•Updated Feb 14, 2019Feb 14, 2019

• compsci-2018

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

  Jupyter Notebook

  •12•4•3•5•Updated Feb 7, 2019Feb 7, 2019

• thermotools

  Public
  Winter is coming...

  Python

  •

  GNU Lesser General Public License v3.0

  •5•12•0•0•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

  •5•8•0•0•Updated Dec 14, 2018Dec 14, 2018

• feature_selection

  Public
  Variational approach to feature selection

  msmvampvamp-scores

  Python

  •0•0•0•0•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

  •1•6•0•0•Updated Sep 10, 2018Sep 10, 2018

• msmrd

  Public
  MSMs coupled with reaction-diffusion dynamics

  Jupyter Notebook

  •1•2•0•0•Updated Aug 9, 2018Aug 9, 2018

• compsci-2017

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

  Jupyter Notebook

  •3•0•0•0•Updated Jan 23, 2018Jan 23, 2018

• compsci-2016

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

  Jupyter Notebook

  •7•1•0•0•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

  •5•10•2•0•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

  •2•1•0•0•Updated Oct 18, 2016Oct 18, 2016

• basissets

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

  Python

  •0•0•0•0•Updated Sep 22, 2016Sep 22, 2016

• coordinates

  Public archive
  Python

  •0•2•10•0•Updated Sep 16, 2016Sep 16, 2016

• mcmm-project

  Public archive
  Jupyter Notebook

  •9•0•0•0•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

  •2•9•12•0•Updated May 25, 2016May 25, 2016

• oom

  Public
  Code for observable operator models

  Python

  •0•0•0•0•Updated Aug 6, 2015Aug 6, 2015