Re: [AMBER] vacuum bubbles generated after heating

From: jani vinod <>
Date: Tue, 13 Apr 2010 14:56:34 +0530

whatever ross suggested is correct first u should try with NVT followed NPT
and occurrence of bubble may mere visualization artifact


On Mon, Apr 12, 2010 at 3:29 PM, 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
AMBER mailing list
Received on Tue Apr 13 2010 - 02:30:02 PDT
Custom Search