[gmx-users] Reducing the dimensionality of my cross correlation matrix
Bailey A.
ab604 at soton.ac.uk
Wed Jul 9 11:40:33 CEST 2014
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
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