Re: [AMBER] Solute and solvent temperatures in mden

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Thu, 10 Jun 2010 18:57:19 -0400

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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Received on Thu Jun 10 2010 - 16:00:05 PDT
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