[gmx-users] Re: Cross-correlation maps

James Starlight jmsstarlight at gmail.com
Tue Aug 28 07:09:32 CEST 2012

Hi Tsjerk!

Normally during analysis of the MD trajectory I've observed frequent
side-chain fluctuations (ps timescale) cased by the temperature motion
of the atoms as well as larger-scale backbone motions ( on the ns

The ps  side-chains motions are known to especially increase total
enthropy of the system in comparison to the backbone dynamics where
such factor is less meaningful. Also there is suggestion that such
enthropy-dominated motions could be functional-relevant due to
possible coperativity of that process ( e.g fluctuations in one side
of protein case increase dynamics in another part of such molecule
without visible pathways between both parts )

The main goal of my study to find out such coperativity in some
proteins. So I want to detect such coperativity in fluctuations of the
side-chains. As I've found the only way to do it is the calculation of
the cross-correlation maps. When I've performed PCA of my 100ns
trajectory and examined filtered.xtc trajectory consisted of first 50
principal components) I didt observed any fluctuations of the
side-chains ( only backbone motions were presented) So I could
calculate only correlations in the backbone atoms motions. Is there
any way to observe such cross-correlations for side chains as well ?


2012/8/27, Tsjerk Wassenaar <tsjerkw at gmail.com>:
> 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?
> Cheers,
> Tsjerk
> On Aug 27, 2012 4:01 PM, "James Starlight" <jmsstarlight at gmail.com> wrote:
> Mark,
> 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?
> James
> 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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