[DFTB-Plus-User] MD simulation of water box using Nose-Hoover thermostat

[Morteza Chehel Amirani]

Dear Bálint

Thanks for the quick check. Yes, that was the reason. I got the box from an
initial force field simulation which was likely not suitable for my MD-DFTB
calculations. I increased the cell size a bit and the temperature
fluctuations became more reasonable.

Sincerely,
Morteza

On Wed, Apr 4, 2018 at 2:56 AM, Bálint Aradi <aradi at uni-bremen.de> wrote:

> Dear Morteza,
>
> > I'm having trouble in the MD simulation of a water box in the PVT
> > ensemble. The MD temperature increases dramatically during the
> > simulation using Nose Hoover thermostat. The temperature
> > fluctuations using Andersen thermostat are fine, however, the
> > trajectory progress is much slower compared with it using the
> > Nose-Hoover thermostat. I'm wondering if you have any ideas on this?
> > Thanks.
>
> You geometry looks somewhat strange. Are you sure, that the periodic
> boundary conditions are correct? If I repeat your geometry with the
> repeatgen tool:
>
> repeatgen geo.gen 2 2 2 > geo.222.gen
>
> I see a suspiciously high density of molecules at the cell boundaries.
> Could that be the reason for the unphysical results?
>
>
>   Best regards,
>
>   Bálint
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>
>
>
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