On Wed, Apr 23, 2008, fatima.chami.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.C6 corr :1.C4 order 2
> vector v2 :2.C6 corr :2.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 27 2008 - 06:07:16 PDT
