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adaptivemd

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

basissets

Basis sets for variational approach for conformational dynamics (VAC)

compsci-2016

Repository for the computational sciences project of 2016/2017

compsci-2017

Repository for the computational sciences software project of 2017/2018

compsci-2018

Repository for the computational sciences software project of 2018/2019

coordinates

decomposed_msms

deep_gen_msm

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

deep_rev_msm

deepmsm

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

deeptime

Deep learning meets molecular dynamics.

feature_selection

Variational approach to feature selection

graphtime

Encoding of transition probabilities with undirected graphical models

ivampnets

markovmodel.github.io

mcmm-project

mdshare

Get access to our MD data files.

molpx

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

msm-theory-sandbox

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

msmrd

MSMs coupled with reaction-diffusion dynamics

msmrd2

msmtools

Tools for estimating and analyzing Markov state models

oom

Code for observable operator models

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

pyemma-workshop

pyemma_ipython

PyEMMA Jupyter Notebooks

pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA

pyfeat

pysfd

pystallone

Python bridge to Java Stallone library