[gmx-users] Re: Cross-correlation maps

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 28 08:52:42 CEST 2012


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.



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

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