AMBER Archive (2007)

Subject: Re: AMBER: correlation time

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 06 2007 - 11:09:07 CST

On Thu, Dec 06, 2007, Tuncel, Aytug wrote:

> By "enthalpy" do you mean the delta_G or individual energies of complex,
> receptor and ligand?

The individual energies, probably. If you are using the "single trajectory"
model, you might want to look at delta values, since some of the high
frequency energy fluctuations would disappear.

> Does the correlation time for relaxation of effective energy fluctuations
> correspond to the time where the correlation function "curve" reaches the
> zero value or do you use a threshold value?

People generally fit the decay curves to an exponential function, and use the
fitted decay times.

...dac

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