Re: [AMBER] vacuum bubbles generated after heating

From: Nicee <>
Date: Tue, 13 Apr 2010 18:23:40 +0530 (IST)

Thanks a lot for the reply. I had used iwrap=1 in my input file, the condition
changed after making it 0.
Thanking you,

> Hello,
> 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
> re-trying...
> 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,
> Jason
> 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
> 352-392-4032

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Received on Tue Apr 13 2010 - 06:00:04 PDT
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