Re: [AMBER] Bubbles during NPT and NVT simulations

From: Bill Ross <>
Date: Thu, 16 May 2019 03:13:54 -0700

One primal cause of bubbles appearing unexpectedly is that one
accidentally applies old box coords to the latest round. I don't know if
the current regime manages to make this impossible, but as Carlos
implies, volume or density would be clues, and you'd see the
discontinuity between one run and the next.

Bubbles in an initial NVT would be normal, but appearing out of nowhere,
if verified, might point to something with your system. What are the
atom counts? I wonder if the system might be too small somehow.


On 5/16/19 2:56 AM, Stefano Motta wrote:
> Dear guys,
> I am running MD simulation for a nanoparticle (NP) in water. Given that the
> NP surface is not regular, I decided to use a simple electrostatic - VdW
> force-field (I found it in literature), and I restrained the conformation
> of the NP to our QM geometry.
> 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. Then I tried to have the heating in NPT (and it
> goes well), but during equilibration (I tried both NPT and NVT) bubbles
> still appears after about 1ns.
> May it be related to the high restraint (5000 kcal/mol−Å2) I imposed on the
> nanoparticle atoms? Is there a way to have a different regulation of
> temperature and pressure for solvent and solute?
> Bests,
> Stefano

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