[gmx-users] Naughty Vacuum Bubble in our Vesicle

[rajat desikan]

Dear Bjorn,

A few thoughts:
1) Are you simulating a coarse grained system (Martini) or an all-atom
system. Isotropic pressure coupling may be more appropriate for a vesicle
because of its spherical symmetry.
2) When you manually added water, did you do it in the vacuum bubble region
only?
3) What is that lateral tension in your vesicle? If your initial vesicle is
tightly packed and has a lot of tension, it may expand to relax, in which
case the internal density of the water may decrease in your production
simulations. (see the PNAS paper from Marrink's group for the procedure to
compute lateral tension).
4) Do you have sufficient water outside the vesicle to hydrate all the
lipids in the outer leaflet?

How about attaching a few snapshots so that we may take a look at them?

Regards,

On Tuesday, October 28, 2014, Björn Sommer <bjoern at cellmicrocosmos.org>
wrote:

> Dear Andre, Rajat & Stephane,
>
> thanks a lot for your light-speed suggestions!
>
>
> @More Water Idea
>
> I'll try to remove as less water as possible in my next try.
>
> But, what bothers me is the fact, that I manually added some water after
> the vacuum bubble was formed and equillibrated again, which resulted in
> another vaccuum bubble with the same or even larger size!
>
> From my understanding, this should not happen. Maybe I overlooked
> something?
>
>
> @Typo in MDP
>
> Thanks Stephane. We used a number of MDPs, we first have to check them
> all, if the typo was only an exception or if it was repeated several times.
> But we will take this into account but I fear, this is not causing the
> vacuum bubble - but we will check it!
>
>
> By the way, we are using GMX 4.6.X - would it make sense to switch to GMX
> 5?
>
> Thanks a lot & best wishes!
> Manuel & Björn
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore