AMBER Archive (2008)

Subject: Re: AMBER: cross time correlation function

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

On Wed, Apr 23, 2008, fatima.chami_at_durham.ac.uk 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
remotely.

...dac
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