[EMAIL PROTECTED] wrote:
Dear Gromacs Users,
My apologies for putting forward a naive question.
Actually, I'm a little confused, is covariance matrix the same as
correlation matrix ??
Names for such procedures vary quite a bit with the kind of field you
work in - I've known scientists, engineers and statisticians to use
different names for the same arithmetic process. In the absence of some
unequivocal mathematical expression for what you're trying to do, it's
hard to guess what you're doing, unfortunately.
I can see below you've been doing some suitable reading, so perhaps you
should try to come up with such a mathematical description of what
you're trying to get your analysis to do. That may give you enough
insight to see how to do it with a GROMACS tool or some other.
Mark
I had been thinking of carryingout DCCM analysis for
my trajectories (20ns each), one for a WT protein and the other a mutant
version. I thought of carrying out the analysis to figureout what are the
residue pairs (if any??) that show correlated/anti-correlated motion
during the course of the MD. Even if I talk about residue pairs I would be
taking the Ca-atoms for each residues. I have checked few articles also:
1. Proteins, 11:205-217 (1991)
2. BMC struct. Biol., 7:73 (2007)
3. Proteins, 65:843-855 (2006)
(Though, in article:2 and 3 they have used inhouse codes for DCCM
construction)
As had been discussed long back in the mailing list (dt: 18 Sept 2007,
raised by Dhananjoy Joshi) people suggested about using:
g_covar -xpma (-xpm) OR g_covar -ascii (using the diagonal coponents etc...)
but for my analysis I find it really difficult to carryout the analysis or
to find any significance coming out of my analysis using g_covar (might be
I'm doing it wrong!!). Thus, I felt I would post my mail in the gmx-list
to invite suggestions from the veterans.
I would really appreciate if someone could guide me carryout the DCCM
analysis properly OR share his expertise.
Warm regards,
Tuhin
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