Thanks all with the quick replies. Please let me know if it would be
helpful for me to send any input files. The output files are a bit large to
send anywhere.
Also, this thread in the archive states a similar negative (and very small)
temperature:
http://archive.ambermd.org/200708/0146.html
--Mickey
On Thu, Jun 10, 2010 at 4:57 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Dear Mickey.
> I think we will need to look at the code, but it is a bug for sure.
>
> How do I know: negative temperatures are non-physical, and 10^10
> obviously is not either.
>
>
> On 6/10/10 6:45 PM, Mickey Richards wrote:
> > I am comparing the Berendsen thermostat (ntt = 1) to Langevin dynamics
> (ntt
> > = 3), for a long simulation (250 ns) of a carbohydrate in explicit TIP3P
> > water in AMBER10, using PMEMD, and GLYCAM06. When I look at the mden
> file
> > generated during my simulations, the temperature for the system and the
> > solute are the same, and the temperature for the solvent takes on values
> of
> > -0.2675E+10. These values are similar for both temperature regulation
> > schemes.
> >
> > 1) Are these negative values for the solvent temperature typical?
> >
> > 2) Is there a way to interrogate whether the solute and solvent are both
> > holding their temperatures appropriately.
> >
> > The first few lines of the mden file are below my signature. Thank you.
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email: mickey18385.gmail.com
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Received on Thu Jun 10 2010 - 16:30:05 PDT
