Thank you very much Sir.
Sajeewa
On Thu, May 23, 2013 at 7:46 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, May 22, 2013, Sajeewa Pemasinghe wrote:
> >
> > In the book 'Molecular modeling principles and applications by Andrew
> > Leach" he describes velocity autocorrelations as shown in
> > autocorrelation.jpg (please see the attached). I think that amber
> > calculates autocorrelation in a similar way.
>
> As noted recently on the list, Amber's analysis routines have no
> straightforward way of calculating velocity autocorrelation functions.
>
> >
> > I have a question about the normalization in equation 7.79 in
> > autocorrealtion.jpg.
> >
> > If our v(0)= a1 i+ a2 j+ a3 k and
> >
> > v(t)= b1 i+ b2 j+ b3 k
> >
> > and v(0).v(0)=a1*a1+a2*a2+a3*a3=norm
> >
> > Can't there be an instance where v(t).v(0)=a1*b1+a2*b2+a3*b3 >
> > a1*a1+a2*a2+a3*a3 ?
> >
> > If that happens there would be correlation values greater than one. So by
> > defining v(0).v(0) as the norm are we assuming that the magnitude of the
> > vector v(t) can never go beyond the magnitude of the vector v(0)?
>
> The correlation function is the *average* of <v(0).v(t)> over the whole
> ensemble. Individual terms in the average might be greater than 1, but the
> average itself is not likely to be -- the assumption is that you have a
> stationary ensemble where <v(t).v(t)> is independent of time.
>
> ...dac
>
>
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Received on Thu May 23 2013 - 05:30:02 PDT
