Hi Sajeewa
if you have 22 carbon alpha you will have (22 * ( 22 -1) / 2 )=231 distances
between them, with the diagonal element 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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Received on Tue Jun 14 2011 - 15:00:03 PDT
