Dear GROMACS and Martini users,
I am working with a membrane-protein system using the Martini 3 force field and would like to calculate the time-dependent spreading area of a protein (or protein condensate) on the membrane surface. Specifically, I want to quantify how the protein’s footprint on the membrane evolves during the simulation. Could anyone suggest robust methods or tools for this analysis?
Here is some context:
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Force field: Martini 3
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MD engine: GROMACS
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System: A protein/condensate interacting with a lipid bilayer (e.g., DIPC/DIPS)
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Goal: Obtain a curve of protein projected area on the XY (membrane) plane vs. time
I am aware of the general principle: project the protein atoms along the membrane normal (Z-axis) and calculate the area they occupy on the XY plane. However, I am looking for practical implementations, preferably ones that work well with Martini 3 systems.
I would greatly appreciate any advice, tool recommendations, or shared scripts.
Thank you in advance for your help!