unanswered Side chain orientation/dynamics in time

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3 months 4 weeks ago #8488 by z.sichaib
Side chain orientation/dynamics in time was created by z.sichaib
Dear Martini users,

I have research & technical related question:

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?

Thank you in advance for your help.

Best,

Zeineb

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