Dear GROMACS users! I'm looking for useful software or VMD plugin for analysis of cross-correlation within of multi-domain protein to study allostery and signal transmission in it.
In practice I have 2 domains joined by long coiled-coiled linker where first domain is ligand sensitive and the second domain has native fluoresce element. I'd like to monitor transduction of conformational changes from first to the second domain during ligand binding seen in 100 ns accelerated molecular dynamics. I've already tried to use VMDs network view plugin analysis based on the cross-correlation computation from the covariance matrix but found only significant correlation within each of domains separately. Does anybody known some alternative solutions for such analysis? Thanks for help, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
