AMBER Archive (2008)

Subject: Re: AMBER: cross time correlation function

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 23 2008 - 12:10:46 CDT

On Wed, Apr 23, 2008, fatima.chami_at_durham.ac.uk wrote:
>
> ("the TCF exceeds one") is what I found and I don't like 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.
>
> ------------------------------------- crosscorrel.ptraj-------------
> trajin ./../stack8w_no_wat.mdcrd
> vector v1 :1_at_C6 corr :1_at_C4 order 2
> vector v2 :2_at_C6 corr :2_at_C4 order 2
> analyse timecorr vec1 v1 vec2 v2 tstep 2 norm out v1_v2_C6C4.out
                                           ^^^^^^

This is your problem: you are normalizing the correlation function to be unity
at time zero. In that case, the TCF can exceed unity (since the "raw" value
at time 0 will be less than one). Try removing this keyword.

...good luck...dac

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