Subject: How to calculate protein spreading area on a membrane over time using GROMACS and Martini 3

User discussions
1

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:

  • Force field: Martini 3

  • MD engine: GROMACS

  • System: A protein/condensate interacting with a lipid bilayer (e.g., DIPC/DIPS)

  • 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!

2

Hi,

I recommend looking into the PyLipID tool ( PyLipID documentation ). I haven’t done your specific analysis, but it sounds like something you can do with either the compute_surface_area() function or by looking into how the number of contacts between your protein/protein condensate and the membrane evolves over time (since you know the diameter of your beads, you could convert the number of contacts into a proxy for surface area)

Cheers!