Not able to get the benzamidine-trypsin trajectory-link https://codeload.github.com/markovmodel/PyEMMA_IPython/zip/devel not working. Kindly provide the trajectory dataset

[anuginu]

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[fabian-paul]

Dear user,

thanks for your interest in PyEmma!

I'm sorry to inform you that the Trypsin-Benzamidine example for the estimation of Hidden Markov Models is no longer available. The Trypsin-Benzamidine example has been replaced with the analysis of simulation data of a pentapeptide. If you want to learn about hidden Markov modelling, please have a look at the new tutorial notebooks. See also the publication Introduction to Markov state modeling with the PyEMMA software

If you're more interested in the analysis of protein-ligand trajectories, I highly recommend to have a look at enhanced sampling techniques and how they can be combined with Markov modeling. As a starting point, I would recommend our publication about TRAM, the Transition-based reweighting analysis method. Notebooks that demonstrate TRAM can be found on the Github page of our recent PyEmma workshop. (memm notebooks).

Best, Fabian