[gmx-users] Naughty Vacuum Bubble in our Vesicle

[Patrick Fuchs]

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.
Ciao,

Patrick

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
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