I am currently working on a system that contains a DMPG bilayer with amyloid beta monomer on one side of the membrane. I generated the system using CHARMM-GUI and oriented the protein using the OPM plug-in. I choose 1:1 as the ratio of DMPG in the upper to lower leaflet. However, after equilibration in GROMACS, I used GridMAT-MD to look at the area per lipid, and saw that I had one leaflet at ~62 sq A and the other at ~57 sq A. The literature value I found for DMPG is 62 sq A per lipid I'm guessing that the protein made one of the layers more tightly packed than the other. How do I adjust the CHARMM-GUI settings to make sure that the area per lipid is even on both sides? Or is there a way to 'fix' the system as it is?
Wojciech Kopec
that makes sense. The protein is asymmetric (resting along headgroups of one leaflet) and the paper I was looking at was for a pure lipid membrane:Article Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic ...
I had difficulty finding literature on area per lipid in protein-membrane systems, which is why I was concerned. Thank you for the clarification.
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