[gmx-users] Naughty Vacuum Bubble in our Vesicle

Patrick Fuchs patrick.fuchs at univ-paris-diderot.fr
Wed Oct 29 09:32:36 CET 2014

Hi Björn,
my five cents. Did you consider constructing the system using MARTINI, 
equilibrating it with artificial pores and then back-map it to all-atom? 
Otherwise, I guess this artificial pore strategy could be applied to an 
all-atom system, but it'd be way more lengthy.


Le 28/10/2014 12:32, Justin Lemkul a écrit :
> 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

Patrick FUCHS
Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
E-mail address: patrick.fuchs at univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs

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