[gmx-users] Re: Cross-correlation maps

[Mark Abraham]

On 28/08/2012 4:09 PM, James Starlight wrote:
> Mark,
>
> Thanks for explanation!
>
>
> 2012/8/27, Mark Abraham <Mark.Abraham at anu.edu.au>:
>
>> Did you construct a correlation matrix from side chain atoms?
> Yes, and there is some degree of correlation between adjacent side
> chains but lack of any cooperativety between distant side-chains. In
> comparison in that protein there were alot of cooperativity in motion
> of the distinct backbones.

Then that might be the conclusion, but that's your judgement to make 
from the full context. It's hardly likely that there'd be magical 
"action at a distance," but motion along the lines of Newton's cradle 
could have been detected and would be fascinating to see in a protein 
(e.g. http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like 
Newton's cradle does require cross-correlation to observe, because of 
the intrinsic asynchronicity, but that would require particular 
plasticity conditions.

>   I suppose that it might be due to the
> relatively limited degree of freedom of the backbones (2 dihedrals
> with 3 minimum conformations) in comparison to the side-chains so the
> correlation in the backbone might be more expected.

Backbone atoms can only move in concert with others, yes.

>
> In addition as I've told you during analysis of filtered.xtc processed
> trajectory I didnt observe any fluctuations of side chains on the
> whole.

Yes, but the amplitude of single-side-chain motions is necessarily 
small, so it doesn't follow that you should observe it in the 
eigenvectors with the largest fluctuations. There's no direct connection 
to the energy required for such motions, either. You should be looking 
at some small peptide systems to learn how to make observations of 
motion you know occurs, before trying to observe hypothesized motion.

>    Finally I've noticed some bugs in the visualistion of the
> side-chains of the structures processed after g_covar  ( e.g
> EDA_average.pdb) In that case the geometry of some side-chains (mainly
> of aromatic rings)  were very distorted. Why this might occur ?

http://www.gromacs.org/Documentation/Terminology/Average_Structure

Mark