[gmx-users] Naughty Vacuum Bubble in our Vesicle

[André Farias de Moura]

Dear Manuel/Björn,

based on your description, I guess that placing some more water after the
bubble has formed may not work as expected, because the bilayer forming the
vesicle might be somehow strained, that's why a suggested stepping back to
the system before equilibration. I think the number of water molecules that
fit inside a vesicle is a typical trial and error problem.

and upgrading software doesn't seem to change anything, since this is
related to the physics of the model, not to the computation itself.

best,

Andre


On Mon, Oct 27, 2014 at 5:13 PM, 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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-- 
_____________

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