[gmx-users] lipids crashed

Justin Lemkul jalemkul at vt.edu
Wed Feb 5 16:21:22 CET 2014

On 2/5/14, 3:33 AM, Albert wrote:
> Hello:
> I am using c36 FF for a mix lipids simulation which contains
> POPC+20%POPG+10%CHOL. The system was equilibrated for more than 100ns. When I
> add a 3nm vacuum layer in each leaflet, and set compressibility to 0 at z
> direction, many lipids was flipped towards solvent environment if I don't
> restrain the head group of the lipids.
> So I am just wondering  how can I solve this problem?

Apparently the introduction of vacuum layers has led to artifacts that affect 
stability.  How thick are the water layers on either side of the membrane?  My 
guess is they are insufficient to avoid the artificial ordering effects that I 
suspected would arise.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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