https://github.com/markovmodel/deeptime

Deep learning meets molecular dynamics.

autoencoder computational-biology computational-chemistry data-analysis deep-learning dimension-reduction machine-learning markov-model python pytorch tensorflow time-series

Last synced: 13 May 2025

https://github.com/markovmodel/pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA

analysis kinetics markov-model md-simulations molecular-dynamics pyemma tutorial

Last synced: 13 May 2025

https://github.com/markovmodel/msmtools

Tools for estimating and analyzing Markov state models

analysis markov-model markov-state-model

Last synced: 13 May 2025

https://github.com/markovmodel/molpx

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

free-energy ipython-notebook jupyter-notebook molecular-dynamics tica visualization widget

Last synced: 28 Oct 2025

https://github.com/markovmodel/pyemma-workshop

pyemma workshop-materials

Last synced: 13 May 2025

https://github.com/markovmodel/mdshare

Get access to our MD data files.

trajectories

Last synced: 13 May 2025

https://github.com/markovmodel/ivampnets

Last synced: 13 May 2025

https://github.com/markovmodel/adaptivemd

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

adaptive hpc markov-model molecular-dynamics-simulation python

Last synced: 13 May 2025

https://github.com/markovmodel/thermotools

Winter is coming...

Last synced: 19 Sep 2025

https://github.com/markovmodel/pyemma_ipython

PyEMMA Jupyter Notebooks

pyemma

Last synced: 13 May 2025

https://github.com/markovmodel/graphtime

Encoding of transition probabilities with undirected graphical models

Last synced: 21 Jul 2025

https://github.com/markovmodel/deepmsm

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

Last synced: 11 Apr 2025

https://github.com/markovmodel/deep_gen_msm

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

Last synced: 02 Mar 2026

https://github.com/markovmodel/pysfd

collective-variables ensemble molecular-dynamics order-parameters visualization

Last synced: 02 Jul 2025

https://github.com/markovmodel/msmrd2

Last synced: 21 Aug 2025

https://github.com/markovmodel/compsci-2018

Repository for the computational sciences software project of 2018/2019

Last synced: 13 May 2025

https://github.com/markovmodel/decomposed_msms

Last synced: 27 Apr 2026

https://github.com/markovmodel/msmrd

MSMs coupled with reaction-diffusion dynamics

Last synced: 18 Jul 2025

https://github.com/markovmodel/deep_rev_msm

Last synced: 20 Aug 2025

https://github.com/markovmodel/msm-theory-sandbox

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

Last synced: 15 Apr 2026

https://github.com/markovmodel/oom

Code for observable operator models

Last synced: 25 Apr 2026

https://github.com/markovmodel/feature_selection

Variational approach to feature selection

msm vamp vamp-scores

Last synced: 22 Aug 2025

https://github.com/markovmodel/stallone

stallone java library

Last synced: 12 Mar 2025

https://github.com/markovmodel/pystallone

Python bridge to Java Stallone library

Last synced: 10 Oct 2025

https://github.com/markovmodel/basissets

Basis sets for variational approach for conformational dynamics (VAC)

Last synced: 02 Sep 2025

https://github.com/markovmodel/markovmodel.github.io

Last synced: 02 Feb 2026