Hi Tsjerk! Normally during analysis of the MD trajectory I've observed frequent side-chain fluctuations (ps timescale) cased by the temperature motion of the atoms as well as larger-scale backbone motions ( on the ns time).
The ps side-chains motions are known to especially increase total enthropy of the system in comparison to the backbone dynamics where such factor is less meaningful. Also there is suggestion that such enthropy-dominated motions could be functional-relevant due to possible coperativity of that process ( e.g fluctuations in one side of protein case increase dynamics in another part of such molecule without visible pathways between both parts ) The main goal of my study to find out such coperativity in some proteins. So I want to detect such coperativity in fluctuations of the side-chains. As I've found the only way to do it is the calculation of the cross-correlation maps. When I've performed PCA of my 100ns trajectory and examined filtered.xtc trajectory consisted of first 50 principal components) I didt observed any fluctuations of the side-chains ( only backbone motions were presented) So I could calculate only correlations in the backbone atoms motions. Is there any way to observe such cross-correlations for side chains as well ? James 2012/8/27, Tsjerk Wassenaar <tsje...@gmail.com>: > Hi James, > > Correlation is covariance normalized to variance. So you'll need the > covariance matrix anyway. But what exactly due you mean with the loss of > information, which you could solve with correlations? > > Cheers, > > Tsjerk > > On Aug 27, 2012 4:01 PM, "James Starlight" <jmsstarli...@gmail.com> wrote: > > Mark, > > Is there any way to calculate such cross-correlations without > calculation of the covariance matrix ( from the MD trajectory > indirectly) ? > I've noticed that after processind of my trajectory with PCA method > some dynamics ( e.g fluctuations of the side-chains) are lost even > when I've analysed filtered.xtc from the first 50 principal > components. How I should analyse possible cross-correlations of the > fluctuations of the side-chains? > > James > > 2012/8/27 Mark Abraham <mark.abra...@anu.edu.au>: > >> On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's > appeared two additional question... > -- > 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 > -- 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
