What temperature and density are reported? What did the density vs time do
during the NPT step, go down or up?
On Thu, May 16, 2019, 5:56 AM Stefano Motta <stefano.motta.unimib.it> 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
>
> --
> ________________________________________________________________
>
> 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 - 03:30:02 PDT
