Dear gromacs users, I posted a similar question the other day, but it was probably too long, so here it is more concisely:
I've taken the ascii output of g_covar and built the 3N x 3N covariance matrix in MATLAB from the 3N^2 x 3 matrix, which I've then normalized to get a 3N x 3N cross correlation matrix. What I'd like is a N x N matrix, and so I've added together the three N x N parts of the 3N x 3N matrix and divided by 3 to get my N x N matrix. However this doesn't look the same as something I'd previously calculated using Ran Friedman's amended g_covar script and I'm trying to understand the discrepancy. Can anyone advise me on what the dimension reduction step should be? I can post my code if that helps. Many thanks, Alistair -- 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.
