AMBER Archive (2009)

Subject: Re: [AMBER] why is TAUTP scaled by "e" ?

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Oct 16 2009 - 08:30:53 CDT

On Thu, Oct 15, 2009, Jose Borreguero wrote:
>
> >From my simulations, it seems that the time evolution of the temperature
> upon heating the system from 300K to 550K with TAUTP=5000psec (very slow
> heating) in the input file results in the system being heated with an
> effective TAUTP=13570=e*5000

I suspect it has nothing to do with "e". The Berendsen procedure changes
the kinetic energy, which is then partitioned into potential energy and
kinetic energy parts. For a harmonic system, changes in <V> are equal
to those in <K.E>; so, other things being equal, the rate of temperature
change will be about two times slower than the value of tautp (since half of
the added kinetic energy will get siphoned off to changes in V). But a
water system (with all water bonds held rigid by SHAKE) will be rather
anharmonic, with a different partitioning between kinetic and potential
energies.

I vaguely recall doing tests 20 years ago on a very harmonic system, which did
have a factor of about 2, but I don't recall what "about" meant in this
context in quantitative terms.

And, as Ross points out, use of the Berendsen thermostat is not generally
recommended.

...dac

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