Bound State of a Protein through kmeans (or GMVAE) Clustering : comp_chem

I am an undergraduate researching in a computational chem lab at UMD. I am done running many HMMM and then AA simulations via CHARMM and NAMD. So far HMMM simulations were converted to AA when the secondary structure seemed stable and the distance to the bilayer was minimal through visual analysis of these respective graphs. In total there are 11 all-atom simulations and 8 HMMM simulations.

All of these simulations are about done running on the supercomputer on campus. When meeting with my PI he directed me to another group member who gave me the files for the GMVAE method linked here. The group member suggested I use the python packages scikit and mdanalysis. It has taken me all day to figure out how to load the files I use into mdanalysis and it is kind of exhausting. Does anyone have any examples of how to do this or any information on how I can get to a clustering of similar “bound” states to the membrane.

Some information on the system is that I am studying the protein magainin and how it binds to the stratum corneum. If there is anything important I left out let me know!

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