Dear all, I am trying to perform the principle component analysis of my protein simulation. Eigen vectors 1-4 cover more than 60 % of fluctuations. When I use -filt option with -b, -e and -skip flags in gmx anaeig, I get an ensemble which represents the fluctuation with the specified intervals (-b and -e) at desired frequency (-skip).
What I want to know is that whether the coordinate frames which I get with the above mentioned approach, really come from time points in the trajectory? Like, if I take a single model from the filtered ensemble, would there be a frame in the trajectory with zero rmsd to this frame OR these filtered frames are 'altered coordinates' from the simulation trajectory to reflect motions calculated by Eigen vectors? Any clarification or reference to the source where I can read more about this would be highly appreciated. Thanks a lot ! Best, Ashu -- 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.
