AMBER Archive (2009)

Subject: Re: [AMBER] thermo, entropy by quasiharmonic method

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Jan 30 2009 - 17:40:38 CST

On Fri, Jan 30, 2009, Carra, Claudio (JSC-SK)[USRA] wrote:

> I'd like to know if there is a way to calculate the entropy, using the
> mass weighed covariance matrix, for each snapshot. So far a managed to
> get the final value, but I'd like to see its change in function of time.

The covariance matrix is itself a time average. It doesn't make any
sense to speak about the covariance of a single snapshot.

Similarly, entropy is a property of the entire ensemble of
configurations that are sampled in a simulation. It is not a
time-dependent (mechanical) property that you can compute snapshot by
snapshot.

...hope this helps...dac

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