Removal of one leaflet causing errors in trajectory

GROMACS version: 2022
GROMACS modification: No

Hi all. I am working on a 10ns simulation of Caveolin in a membrane bilayer. I’m running depletion/enrichment analysis on just the cytosolic leaflet with the MDAnalysis library. To do so, I have processed my original trajectory to remove the extracellular leaflet as well as water and any ions. Unfortunately, once I remove the extracellular leaflet using trjconv (supplying a suitable index file and a topology file with this leaflet already removed), I am seeing really odd changes to the remaining leaflet and the protein. I have not applied any other fitting to the trajectory. For one of my triplicates, the remaining layer collapses to form a kind-of bilayer and the protein is pushed out of the membrane and just ‘surfing’ around on it (Image 2). I have highlighted some of the headgroups to make this more visible. On the other two, the protein remains in the lipid layer, but is moving a lot in the z-axis and falls out of the membrane a few times during the trajectory (Image 3). The topology files from all of the runs are totally fine (Image 1). Any insight to what may be causing this and how to fix it would be greatly appreciated!

I was only able to embed 1 image as I am new to the forum. Here are images 2 and 3 (where the errors are occurring).

I don’t really understand why you have to remove one of the leaflets, the water and the ions. I’m not surprised that causes these issues. You are simulating one leaflet and the protein in vacuum. You will lose everything (?) that keeps the system stable. As you also removed ions you might also have a net charged system, is that right? Any analysis on a system like this would be very arbitrary anyway, since you would have to prove that your changes don’t affect the behaviour of the system.