Example/tutorial for dealing with MD trajectories

[pojeda]

Hi,

I have been exploring the documentation of Deeptime and I haven't found any example for dealing with MD trajectories from common packages like AMBER, GROMACS, NAMD, etc. PyEMMA was more complete in this sense. I wonder if you have tutorials or examples on how to do an analysis such as TICA with data coming from MD simulations? Thank you.

[clonker]

Hi, we have a series of notebook dealing with deeptime for MD data: https://github.com/markovmodel/pyemma-workshop
That being said it does not cover how to load large amounts of data chunk-wise. For that you (currently, I still want to add that at some point...) would have to call partial_fit on the methods that support it.