[AMBER] Bubbles during NPT and NVT simulations

From: Stefano Motta <stefano.motta.unimib.it>
Date: Thu, 16 May 2019 11:56:24 +0200

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?


Stefano Motta PhD
Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
*Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
Università degli Studi di Milano Bicocca
Department of Earth and Environmental Sciences
Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
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Received on Thu May 16 2019 - 03:00:02 PDT
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