[gmx-users] normalized

Mark Abraham mark.j.abraham at gmail.com
Sat Dec 17 23:25:47 CET 2016


We don't have anything to go upon... this could be a code bug or a usage
bug. How did you generate your input file? Have you inspected your input
file to check for sanity? (e.g. with gmx dump, remembering that the first
frame or two are different, see gmx covar -h) What is the whole terminal
output of both stages?


On Sat, Dec 17, 2016 at 10:30 AM Lovas, Sandor <SandorLovas at creighton.edu>

> 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."
> Sandor
> --
> ______________________________________
> 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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