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From: Sajeewa Pemasinghe <sajeewasp.gmail.com>

Date: Tue, 14 Jun 2011 19:48:05 -0400

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
*

*> >> _______________________________________________
*

*> >> AMBER mailing list
*

*> >> AMBER.ambermd.org
*

*> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> >
*

*> >
*

*> _______________________________________________
*

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*

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*>
*

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Received on Tue Jun 14 2011 - 17:00:04 PDT

Date: Tue, 14 Jun 2011 19:48:05 -0400

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:

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Received on Tue Jun 14 2011 - 17:00:04 PDT

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