[gmx-users] CHARMM-GUI Membrane building problems

Justin Lemkul jalemkul at vt.edu
Fri May 6 12:52:07 CEST 2016

On 5/5/16 11:41 AM, John Smith wrote:
> 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.

Are the starting coordinates sane?  How quickly does the problem occur?  Any 
visual clues as to what's going on from watching the trajectories?  I have never 
seen such a thing happen, and the force required for such a displacement would 
be rather large.


> Sincerely,
> John


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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