> 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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 14 2011 - 15:00:04 PDT
