GROMACS version: 2023.2
GROMACS modification: Yes
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Good day!
I am currently running several MD simulations of a protein-protein complex where one protein, the receptor, is a trimer and the other a theraphotoxin. I would like to ask for inputs on possible thermodynamic analyses on the completed MD simulations. I was thinking of RDF and binding energy, but I do not have that much of a grasp on what possible thermodynamics analyses I can do with this system.
I followed this tutorial for my MD simulation.
Thank you in advance!