u/Smooth-Entrance-3148

I recently worked on a small project as part of my course in QC Modelling which has me performing MD on a protein (Lysozyme and some others), and then running the results through an MSM( Markov State Model ) with pyemma and deeptime.

The results aren't really spectacular mainly because I didn't have access to a cluster then(and neither do I have it now), and my MD trajectories were too small for it.

I have been wanting to extend it into a full length project (by length I mean something that is more than popping an MD traj into a MSM tutorial I found online). Would anyone suggest any extensions to the project?

Would love to hear your thoughts and maybe any literature you'd recommend me to read up on?