[gmx-users] g_covar -ref

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 18 17:51:04 CET 2010

Hi Vijaya,

Well, to start with that will be something as calculating the
'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith
atom of the conformation x and the reference structure r and the sum
is over time/observations. In the case of no variation in xi, the
value you get will still be finite, in stead of zero, as would
probably be most meaningful.
Now for the covariances, there's a bit more to it. The covariance is
the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
there is no correlation, the deviations about the mean are random and
average out to zero. But with the deviations against a reference, that
is not the case. So the results should be regarded meaningless, unless
you have a good reason for doing so, and come with a solid
justification. Okay, there may be a purpose, but I'll leave that to
your imagination :)

Hope it helps,


On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
<vijaya65 at hotmail.com> wrote:
> Hi
> Has anyone studied the effect of using different reference structures,
> not the average structure, when carrying out PCA.  Does it make sense to use
> a structure besides the average to calculate the covariance matrix?
> Thanks
> Vijaya
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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