Hi George,
Thank you very much for the quick reply. My trajin file looks like below.
trajin amn1122_xd1_umbrella.mdcrd
trajin rerun_1122_300ps_more_umbrella.mdcrd
vector v1 :993.CG corr :996.N
analyze timecorr vec1 v1 vec2 v1 tstep 1 norm out 1122updated.autocorr
Thank you
Sajeewa Dewage
On Wed, May 22, 2013 at 5:20 PM, George Giambasu <giambasu.gmail.com> wrote:
>
> > 1) What is the reason for the first 500ps of both plots for not being
> > identical? Is it because the normalizing factors for the two
> > auto-correlations being different?
>
>
> Each point of a correlation function is an ensemble average over the whole
> trajectory. The difference you get is due to the fact that you use
> different structural ensembles (that partially overlap).
>
>
> >
> > 2) Could anyone please tell me the equation they use in amber to
> > calculate
> > the time-autocorrealtion functions?
>
>
> There are several types of correlations functions one can compute. Show us
> the ptraj command you used.
>
> George
>
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Received on Wed May 22 2013 - 14:30:04 PDT
