AMBER Archive (2006)

Subject: Re: AMBER: RMS FLUCTUATIONS

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 15 2006 - 23:09:53 CDT

On Thu, Jun 15, 2006, Jiang Jianwen wrote:
>
> Note that in a NVT ensemble with temperature coupling, T fluctuates.

It is more correct to say that the kinetic energy fluctuates (as it must);
the thermodynamic temperature is related to the *mean* kinetic energy, not to
the instantaneous kinetic energy at any instant in time. Tf you thermostat is
working well, the temperature determined from the mean kinetic energy should
be very close to the target temperature (i.e. the temperature of the
hypothetical bath that is in thermal equilibrium with your system.)

(Note also that your formula will estimate the heat capacity of your system;
you still have to convert that to a per-gram or per-mole basis to compare to
any typical experimental value.)

...good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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