[gmx-users] Naughty Vacuum Bubble in our Vesicle

Justin Lemkul jalemkul at vt.edu
Tue Oct 28 12:32:58 CET 2014

On 10/28/14 6:23 AM, Björn Sommer wrote:
> Dear Rajat,
> Dear Andre,
> Dear all,
> thanks again for your help.
> 1) I'm simulating an united atoms model and isotropic pressure is used, not
> coarse-grained (this would be indeed more simple, because faster and much more
> examples are available).
> 2) Yes, I added additional water bubbles of different sizes only in the vacuum
> region.
> 3) I don't know the lateral tension yet, but I'll try to compute it and hand in
> this information later.
>> 4) Do you have sufficient water outside the vesicle to hydrate all the
>> lipids in the outer leaflet?
> 4) Yes, there should be enough water. I think, that this is currently not the
> problem, but we will keep this in mind.
> In addition, you find two snapshots, one of the vacuum bubble and one of the
> inner lipid layer coated by water:
> http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf
> (Sorry, I just had to do this joke, Manuel! - Björn ;-)
> In addition I'm running a minimization run right now with a lot more water
> inside and will continue to equillibrate soon, as far as I get an useful result,
> we will inform you.

Does the size of the vesicle itself change at all?  My thought is that this 
could simply be a force field issue; if the surface tension in the vesicle is 
wrong, then if it gets larger over time, there's only a finite amount of water 
in the center of the vesicle, so bubbles develop.

Apologies if I've missed relevant information; I've been following the thread 
but have not had time to study it very closely.



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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