Re: [AMBER] vacuum bubbles generated after heating

From: Jason Swails <>
Date: Mon, 12 Apr 2010 06:11:45 -0400


It is possible that the 'vacuum bubbles' are merely visualization
artifacts of reimaging (i.e. wrapping molecules back into the original
box), though is perhaps unlikely for a simple heating. It is also
possible that maybe you don't have enough water molecules to maintain
a good density with the volume you're trying to run at? If this is
the case, perhaps run a quick NPT heating simulation to equilibrate
the density and try with NVT again to make sure that this problem goes
away? It may also be worth trying to rebuild the system in leap and

Also, did you minimize the system prior to trying this? Other than
these, I'm not sure what else can/should be done... Perhaps others can
chime in with their advice.

All the best,

On Mon, Apr 12, 2010 at 5:59 AM, Nicee <> wrote:
> Dear all,
> I am trying to simulate a protein. I first minimized it and now trying to
> equilibrate the system. The first md run was for heating the system. During this
> step i tried to raise the temperature gradually from 0K to 300K with 10k
> increase in every 20ps at NVT with Shake on hydrogen bonds for a total time of
> 1.2 ns and a cut off=12A. After this step i visualized the structure in vmd and
> found that vacuum bubbles were generated in the system. So i searched in the
> mailing list archive for the same and found that the system should be heated
> slowly over 20ps or so with ntb=1 and ntt=3 and then it should be equilibrated
> at NTP with ntb=2 and ntt=3. So i  changed the protocol and now heated the
> system slowly from 0K to 100K with 10K increase for every 5ps for a total time
> of 100ps at NVT with shake on hydrogen bonds. But even after this short slow
> heating the system showed appearance of similar vacuum bubbles. I had planned to
> equilibrate the system after this step at NPT with tempi=100 and temp0=300 and
> shake on hydrogen bonds. But the structure showed vacuum bubbles before that so
> i didn't continued it. I request to kindly suggest a reason for the generation
> of vacuum bubble and what should i do to avoid it.
> Thanking you.
> Nicee.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Apr 12 2010 - 03:30:03 PDT
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