Re: [AMBER] Solute and solvent temperatures in mden

From: Adrian Roitberg <>
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
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Received on Thu Jun 10 2010 - 16:00:05 PDT
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