I have a coarse-grained trajectory with Martini Force Field of a protein (5 transmembrane helices) embedded in a bilayer with 6 types of lipids.
I am interested in lipid-protein interactions.
I would like to characterize the side-chain dynamics/orientation of some key residues in time:
* if their side chains are pointing toward the membrane, ---> in this case, they can interact with the lipids
* or point toward the opposite side (inside of the protein/buried), ---> interaction with the lipids is not possible.
Is there a way to characterize this? a quantity to measure?