[gmx-users] CHARMM-GUI Membrane building problems

John Smith nimzster at yahoo.com
Thu May 5 10:13:45 CEST 2016

Hello All,
I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with CHARMM-GUI. The process seems to be fairly straightforward. Unfortunately, there are problems with the resulting configuration of the membrane. After running the equilibration scripts provided as part of the Charmm-GUI output download, with the default MDP files provided, I see that several of the lipids are resting in horizontal positions on the "top" of the bilayer (e.g. a DOPC molecule with chains pointing sideways instead of into the bilayer). So, I tried more strongly position-restraining the head-groups of all three molecule types in z, and re-ran all the equilibrations from the beginning. Unfortunately, I still see a couple Cholesterol molecules horizontally on the top of the bilayer. Any suggestions as to why this might be, and how one might prevent it? I could weakly position restrain the ends of the lipid chains in z as well, but I am not sure whether this might have unwanted side effects.

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