[gmx-users] CHARMM-GUI Membrane building problems

[John Smith]

Hello,

I am resending this message from my Gmail account, as it appears that
messages sent from my Yahoo account are going to spam. Apologies if you
have already seen this.

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 DOPC and 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 during the equilibration.

Sincerely,
John