[gmx-users] lipids crashed

Justin Lemkul jalemkul at vt.edu
Wed Feb 5 16:53:34 CET 2014

On 2/5/14, 10:49 AM, Albert wrote:
> On 02/05/2014 04:19 PM, Justin Lemkul wrote:
>> 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.
> it is 3nm for the the water layer in each side of the membrane. The system was
> initially built from charmm-gui, the default thickness is 1.5nm....
> I thought my water is more than enough.....:(

Your results would suggest otherwise.  Introducing a vacuum layer close to a 
membrane introduces all sorts of surface effects and perturbations.



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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