[gmx-users] Naughty Vacuum Bubble in our Vesicle

Björn Sommer bjoern at CELLmicrocosmos.org
Mon Oct 27 20:13:55 CET 2014

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 

@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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