[gmx-users] normalized overlap

Lovas, Sandor SandorLovas at creighton.edu
Thu Dec 15 00:32:59 CET 2016

I am trying calculate the degrees of overlap of subsets of a simulation to the whole trajectory by following the explanation in the manual of gmx anaeig:

"When -v, -eig, -v2 and -eig2 are given, a single number for the overlap between the covariance matrices is generated...."

Although, it does not make any difference whether I use or not 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."

Has anyone else found this problem?


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