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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
