AMBER Archive (2008)

Subject: Re: AMBER: cross time correlation function

From: David A. Case (
Date: Wed Apr 23 2008 - 10:55:07 CDT

On Wed, Apr 23, 2008, wrote:
> is there a way to work out the cross time correlation function (TCF) using the
> unit vector of each inter-atomic vector ...cause the TCF exceeds one.

In the "analyze timecorr" command, you can make vec1 different from vec2, and
you will get cross-correlation functions. The examples section in the ptraj
manual has an example of this.

However, I'm guessing that I don't really understand what you want. These
auto- or cross-corrrelation functions are averages of Legendre polynomials (of
order 2 by default), and hence should never be greater than unity. I can't
tell from your statement ("the TCF exceeds one") if this what you found and
you don't like it, or if this is what you expect, and you are *not* seeing it
in the ptraj output. In any event, you will need to give details about
exactly what commands you tried if there is much hope of getting real help

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