Hello. I am looking far and wide to learn how to simulate my ion channels to understand which of the 5 conformations I got from my cryo-EM experiments are the most stable, and possibly assign the likely trajectory of conformational transitions between these 5 structures.

Now, I have a general overview of MD simulation workflow, but I do not have in-depth knowledge of how to run it. I do have a Linux workstation (8 x RTX A6000, 48 GB RAM each) at my disposal and I can install all the software needed.

Is there anyone who could send some tutorials, google collab notebook links so that I can try and do this? I would first start on one structure and work from there.

I really appreciate your help as I do not have a strong MD background. I am a cryo-EM enthusiast trying to learn MD as well :)