[gmx-users] Naughty Vacuum Bubble in our Vesicle
bjoern at CELLmicrocosmos.org
Tue Oct 28 11:23:29 CET 2014
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
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.
Manuel and Björn
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