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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
