Holes in the membrane during equilibration – User discussions

GROMACS version: 2021.3
GROMACS modification: No

Hi all,

I created a Martini 2.2 PC/PE/CHOL membrane-protein system solvated in water, energy minimized the structure, ran a short NVT equilibration, and am equilibrating it at 1 bar and ~310 K conditions with 50 kJ/mol/nm position restraints on the protein to prevent deformation. I have noticed that after the first 25 ns of equilibration, a hole emerges in the membrane. Now that I am 750 ns into the NPT equilibration, the hole in the membrane remains. I am wondering if anyone else has seen these holes emerge during the equilibration process and if they will eventually close on their own given more time to equilibrate or if there is a way to otherwise ensure that the membrane remains intact. As shown in the pictures below, I have seen these holes emerge even as I varied the size of the membrane somewhat. Thank you for any suggestions.

Screen Shot 2023-05-11 at 11.16.19 AM

Screen Shot 2023-05-11 at 11.16.44 AM

Screen Shot 2023-05-11 at 11.16.29 AM

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