[gmx-users] lipids crashed

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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