Thank you very much for spending your time on me.
On Tue, Jun 14, 2011 at 5:42 PM, Mariano Rech <mariano.rech.gmail.com>wrote:
> > Hi Sajeewa
> >
> > if you have 22 alpha carbons you will have (22 * ( 22 -1) / 2 )=231
> > distances between them, with the diagonal elements representing the
> > variances (or standard deviation to the second) of these distances
> >
> > the elements of this matrix will be as in
> > http://mathworld.wolfram.com/CovarianceMatrix.html
> >
> > Anyway I do not know how these distances are ordered by ptraj, but if you
> > get a look at the ptraj code you could see by yourself
> >
> > hope this help
> >
> > Mariano
> >
> >
> > 2011/6/14 Sajeewa Pemasinghe <sajeewasp.gmail.com>
> >
> >> ---------- Forwarded message ----------
> >> From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> >> Date: Mon, Jun 13, 2011 at 6:48 PM
> >> Subject: Interpreting the distance covariance matrix
> >> To: amber.ambermd.org
> >>
> >>
> >> Hi,
> >>
> >> I have run a distance-covarinace analysis for 22 alpha carbon atoms
> >> specified by the mask1. I thought I would get a 22 by 22 symmetric
> matrix
> >> where the diagonal elements correspond to the variances. Instead I got a
> >> 231
> >> by 231 symmetric matrix. I am having a very hard time interpreting this.
> >> This is my first time running a distance covariance calculation in
> amber.
> >> I
> >> would really appreciate if you could give me some helpful explanation in
> >> interpreting the structure of 231 by 231 matrix.
> >>
> >> Best Regards
> >> Sajeewa
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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Received on Tue Jun 14 2011 - 17:00:04 PDT
