On 28/08/2012 3:09 PM, James Starlight wrote:
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
time).
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 )
So you're looking for correlated motion of atoms distant in space. That
will appear as off-diagonal entries in the correlation matrix. Think
about what sort of correlation matrices and eigenstructure you would
expect for a system of a small number of SHM oscillators under different
sorts of correlation conditions. Then worry about proteins.
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.
Cross-correlation is an analysis distinct from looking at off-diagonal
(a.k.a. "cross") elements of a correlation matrix.
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 ?
Did you construct a correlation matrix from side chain atoms?
Mark
James
2012/8/27, Tsjerk Wassenaar <[email protected]>:
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" <[email protected]> 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 <[email protected]>:
On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's
appeared two additional question...
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