[gmx-users] Reducing the dimensionality of my cross correlation matrix
Bailey A.
ab604 at soton.ac.uk
Wed Jul 9 15:31:49 CEST 2014
I answered my own question and solved this, just a typo in my code. If anyone else has the same issue, drop me a line.
I'll put a script up on MATLAB central at some point too.
Alistair
-----Original Message-----
From: Bailey A. [mailto:ab604 at soton.ac.uk]
Sent: 09 July 2014 10:40
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Reducing the dimensionality of my cross correlation matrix
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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