[gmx-users] DCCM

[tuhin at iitk.ac.in]

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 ?? 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