Re: [AMBER] Bubbles during NPT and NVT simulations

From: David A Case <>
Date: Thu, 16 May 2019 08:05:25 -0400

On Thu, May 16, 2019, Stefano Motta wrote:
>The problems concern the equilibration of the solvent (I simulate the
>system in a octahedral water box). I first minimized the system, and then
>have a short heating followed by an equilibration part. I tried to do the
>heating in NVT and then the equilibration in NPT but in the first part of
>heating bubbles appears.

Just one more point here: what is your evidence that you have bubbles?
Some visualization? If so, be sure that you have imaged the coordinates
(with cpptraj) before looking at the result.

Of course, if you have already done the imaging, then you can ignore
this comment. But failing to image things before visualization is an
easy mistake to make.

>May it be related to the high restraint (5000 kcal/mol−Å2)

Consider reducing the restraint by about three orders of magnitude. I'm
a little surprised that you can even run dynamics with that large a
force constant.

...good luck....dac

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Received on Thu May 16 2019 - 05:30:02 PDT
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