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34 repositories

adaptivemd
Public archive
A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
python markov-model hpc
python markov-model hpc molecular-dynamics-simulation adaptive
Python
•
GNU Lesser General Public License v2.1
•8•17•17•2•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
•6•32•4•1•Updated Nov 22, 2023Nov 22, 2023
PyEMMA
Public archive
🚂 Python API for Emma's Markov Model Algorithms 🚂
python markov-model hmm
python markov-model hmm time-series analysis molecular-dynamics bayesian-methods tica hidden-markov-model markov-state-model
Python
•
GNU Lesser General Public License v3.0
•126•339•57•0•Updated Sep 11, 2023Sep 11, 2023
ivampnets
Public
Python
•2•25•1•0•Updated Feb 28, 2023Feb 28, 2023
msmtools
Public
Tools for estimating and analyzing Markov state models
markov-model analysis markov-state-model
markov-model analysis markov-state-model
Python
•
GNU Lesser General Public License v3.0
•27•41•0•0•Updated Aug 15, 2022Aug 15, 2022
pyemma-workshop
Public
workshop-materials pyemma
workshop-materials pyemma
Jupyter Notebook
•
GNU Lesser General Public License v3.0
•8•32•2•0•Updated Feb 24, 2022Feb 24, 2022
decomposed_msms
Public
Jupyter Notebook
•0•2•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
•3•8•0•0•Updated Oct 19, 2021Oct 19, 2021
msmrd2
Public
C++
•1•5•0•0•Updated Mar 18, 2021Mar 18, 2021
PyEMMA_IPython
Public
PyEMMA Jupyter Notebooks
pyemma
pyemma
Jupyter Notebook
•12•13•2•0•Updated Jan 28, 2021Jan 28, 2021
PySFD
Public
visualization molecular-dynamics ensemble
visualization molecular-dynamics ensemble order-parameters collective-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-model tutorial analysis
markov-model tutorial analysis molecular-dynamics kinetics md-simulations pyemma
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•34•86•3•0•Updated May 29, 2019May 29, 2019
deeptime
Public
Deep learning meets molecular dynamics.
python markov-model machine-learning
python markov-model machine-learning deep-learning time-series tensorflow computational-biology pytorch computational-chemistry autoencoder
Jupyter Notebook
•
GNU Lesser General Public License v3.0
•41•189•5•0•Updated May 3, 2019May 3, 2019
molPX
Public
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
visualization widget jupyter-notebook
visualization widget jupyter-notebook molecular-dynamics ipython-notebook tica free-energy
Python
•
GNU Lesser General Public License v3.0
•4•44•12•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•14•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•9•0•0•Updated Dec 14, 2018Dec 14, 2018
feature_selection
Public
Variational approach to feature selection
msm vamp vamp-scores
msm vamp vamp-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
•2•5•0•0•Updated Sep 10, 2018Sep 10, 2018
msmrd
Public
MSMs coupled with reaction-diffusion dynamics
Jupyter Notebook
•1•3•0•0•Updated Aug 9, 2018Aug 9, 2018
compsci-2017
Public archive
Repository for the computational sciences software project of 2017/2018
Jupyter Notebook
•2•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•10•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

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Markov model

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34 repositories

adaptivemd

mdshare

PyEMMA

ivampnets

msmtools

pyemma-workshop

decomposed_msms

deepmsm

msmrd2

PyEMMA_IPython

PySFD

deep_rev_msm

pyemma_tutorials

deeptime

molPX

compsci-2018

thermotools

graphtime

feature_selection

deep_gen_msm

msmrd

compsci-2017

compsci-2016

variational

msm-theory-sandbox

basissets

coordinates

mcmm-project

pytram

oom

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34 repositories