[gmx-users] Re: About Temperature coupling and Energy Transfer....

Justin Lemkul jalemkul at vt.edu
Wed Nov 28 13:28:17 CET 2012

On 11/28/12 12:11 AM, cyberjhon wrote:
> Dear Justin
> Thanks for your answer.
> I know what you mean, but the problem is that this is not
> a possible physical (real) behaviour.
> If the temperature is not controlled as you said, the energy should continue
> growing not stop, but in these case after 50ps it reaches some kind of
> equilibrium
> and stabilize.
> So why this is happening? Can you give me with a Physical or
> and Algorithmic answer?

I'm guessing a bit here, because what you're doing is something that these 
algorithms were not intended to do.  You have a warm solvent and a protein whose 
temperature is unregulated, so the protein acts as a heat sink and has energy 
transferred into it in an uncontrolled way.  Maybe the algorithm finds a happy 
place at the temperature where it stabilizes, or maybe it's a failure of the 
thermostat that doesn't lead to a fatal error.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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