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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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