[AMBER] vacuum bubbles generated after heating

From: Nicee <nicee.srivastava.imtech.res.in>
Date: Mon, 12 Apr 2010 15:29:32 +0530 (IST)

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.


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Received on Mon Apr 12 2010 - 03:00:02 PDT
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