Re: minimization and water bubbles

From: Axel Kohlmeyer (
Date: Thu Jun 14 2012 - 21:49:40 CDT

On Thu, Jun 14, 2012 at 10:33 PM, Dr. Eddie <> wrote:
> Hi all,
> I have a small (2700 atom) protein that is solvated and should be very close
> to correctly folded. When I run the minimization on the solvated system it
> seems to form a large air bubble. I am using pbc and waterWrap on and at the
> end of my config file it has:
> minimize            800
> reinitvels          310
> run  20000000
> In the output from the run after the energy it prints:
> Yet the protein seems to be very cold and there is a large air bubble in the
> system. This is not the "fake" bubble due to pbc (I see that one as well).
> Even after 2 ns the bubble is still almost perfectly spherical. Shouldn't it
> have reheated and given me something similar to when I don't minimize? Has
> anyone had this problem and knows what I am doing incorrectly?

you are probably running with constant volume.
check your system's density, almost all tools to
solvate molecules leave some little vacuum to
avoid overlaps (which will lead to atoms being
"shot" through the simulation cell and the simulation
crashing). if you run long enough with constant
volume, you'll get a little vacuum bubble.


> The protein's structure is almost identical after minimization yet there is
> a large change in pressure and potential energy during minimization so I
> assume almost all the minimization is coming from the water. Also I don't
> see the bubble when I don't minimize.
> I greatly appreciate any help. Thanks in advance!
> Eddie

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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