[gmx-users] Naughty Vacuum Bubble in our Vesicle

Björn Sommer bjoern at CELLmicrocosmos.org
Tue Oct 28 11:23:29 CET 2014

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:


(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.

Best wishes,
Manuel and Björn

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