[gmx-users] normalized

Lovas, Sandor SandorLovas at creighton.edu
Sat Dec 17 00:29:58 CET 2016

I have asked this question a few days back; I try one more time:

When I am trying calculate the degrees of overlap of subsets of a
simulation to the whole trajectory by following the explanation in the
manual gmx anaeig:
"When -v, -eig, -v2 and -eig2 are given, a single number for the
overlap between the covariance matrices is generated...."

For me, it does not make any difference whether or not I use the "-eig" 
and "-eig2" inputs, the results for normalized overlap are the same. In
other words, the normalized overlap is not calculated by using the
equation given in the manual:

"normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
where M1 and M2 are the two covariance matrices and tr is the trace of
a matrix."

Dr. Sandor Lovas, Professor            
Department of Biomedical Sciences      
Creighton University                   
2500 California Plaza,                 
Omaha, NE 68178, USA 

Phone: 402-280-5753
Fax:   402-280-2690                 

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