[gmx-users] Re: Cross-correlation maps

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Aug 27 21:19:05 CEST 2012

Hi James,

Correlation is covariance normalized to variance. So you'll need the
covariance matrix anyway. But what exactly due you mean with the loss of
information, which you could solve with correlations?



On Aug 27, 2012 4:01 PM, "James Starlight" <jmsstarlight at gmail.com> wrote:


Is there any way to calculate such cross-correlations without
calculation of the covariance matrix ( from the MD trajectory
indirectly) ?
I've noticed that after processind of my trajectory with PCA method
some dynamics ( e.g fluctuations of the side-chains) are lost even
when I've analysed filtered.xtc from the first 50 principal
components. How I should analyse possible cross-correlations of the
fluctuations of the side-chains?


2012/8/27 Mark Abraham <Mark.Abraham at anu.edu.au>:

> On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's
appeared two additional question...

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