[gmx-users] Re: Cross-correlation maps

[Tsjerk Wassenaar]

Hey,

In addition to Newton's cradle, there's also Columbus' egg. To make it
stand, you smash it slightly, pressing one end. If you do PCA on that,
you'll find a collective motion involving both the smashed end as well
as the opposite, unscathed end. That accounts for the greater part of
the global, end-to-end collective motions you see when you analyze the
backbone. You don't have that when looking at the more subtle side
chain motions.

Cheers,

Tsjerk


On Tue, Aug 28, 2012 at 8:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

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