[gmx-users] Naughty Vacuum Bubble in our Vesicle

[André Farias de Moura]

Dear Manuel/Björn,

I think Patrick has a point, an artificial pore should allow the solvent to
equilibrate itself across the bilayer, but you need to choose atomistic and
coarse grained force fields that yield very close areas per lipid (for
planar bilayers, for instance), otherwise the atomistic and coarse grained
vesicles will most likely relax to different curvatures and lipid packing,
and then the pore won't be much useful as a strategy to relax the pore, you
will probably end up with the wrong hydration inside the vesicle (either
too few or too many water molecules).

best,

Andre


On Wed, Oct 29, 2014 at 6:32 AM, Patrick Fuchs <
patrick.fuchs at univ-paris-diderot.fr> wrote:

> 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
> 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
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>


-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090