Mark, Thanks for explanation!
2012/8/27, Mark Abraham <mark.abra...@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 ? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
