Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post:
I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.611 0.638 0-10ns 0.616 0.650 0-20ns 0.646 0.671 0-30ns 0.656 0.678 0-40ns 0.659 0.683 0-50ns 0.873 0.919 0-60ns 1.000 1.000 0-70ns 1.000 1.000 0-80ns 1.000 1.000 0-90ns 1.000 1.000 0-100ns 1.000 1.000 0-110ns = Ttot Regards, Miguel -- 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