AMBER Archive (2006)


From: David A. Case (
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


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to