From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 23 2009 - 10:19:42 CDT
On Thu, 2009-07-23 at 18:48 +0400, Mikhail Suyetin wrote:
> Hi all.
> I'am developing biological system and I need to keep T=309,75 (36.6
> degrees centigrade) strongly.
why??? and particularly, why so exact?
> The question is may I set RescaleFreq of temperature =1? (below sample
> of .namd file)
> -------------
> rescaleFreq 1
> rescaleTemp $temp
> -------------
> I clearly understand that I'll get neither NVE nor NVT ensemble. Can
> anybody interpret essense of such processes?
it is a very unrealistic setup. temperature is not a well defined
property for a system with a finite number of particles. we usually
assume equipartitioning. rescaling in every step will artificially
slow down all processes that would happen due to the natural
fluctuations.
just consider the extreme case of a single harmonic oscillator.
its kinetic energy (and thus its temperature) _has_ to fluctuate
between T=2xT_avg and T=0K. a typical MD setup is just many more
of those and they are not oscillating at the same frequency.
cheers,
axel.
> --
> Sincerely yours,
> Mikhail Suyetin
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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