[gmx-users] Re: Cross-correlation maps

[James Starlight]

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. 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.

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.  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 ?