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

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 23:47:37 CET 2012

On 11/20/12 5:42 PM, jhon michael espinosa duran wrote:
> Hi all.
> I am trying to simulate a protein initially at 0K
> in water at 310K. I couple the water to 310K with
> tc=0.5 and the Protein is decouple tc=-1.
> The idea is analyze how is the transfer of energy from the
> water to the protein.
> The interesting thing is that after 200ps the temperature of the
> water is constant (obviously) at 310K and the temperature of the protein
> goes up 628K!!!!!!
> I test the same system for different water temperatures 100K, 150K and 200K
> and the protein temperature always goes up 400K, 475K and 525K, respectively
> Can some one give an explanation?

It's because you have tau_t set to -1.  That tells mdrun not to control the 
temperature of the protein.  You've got warm solvent around a cold protein with 
an unregulated temperature, so the system is rapidly transferring heat into the 
protein and mdrun believes that's normal.



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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