Hi,
On Friday, 31. August 2007 05:14, Arneh Babakhani wrote: > Can anyone briefly recommend a procedure for calculating the correlation > matrix (not the diagonalized covariance matrix, as done by g_covar) of a > specified group? > > In particular, I'm looking to calculate the covariance matrix, as specifed > in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry of > the matrix is defined as the correlation between the i-th and j-th atom: > > c_ij = <delta r_i> <delta r_j> > > where delta r is the deviation of i from its average position, averaged > over the ensemble. > > Or, is there a way to use g_covar and suppress the diagonalization step, > so as to obtain only the translation correlation matrix??? (I couldn't > find anything to this effect in the manual). take a look at Generalized Correlation for Biomolecular Dynamics from Lange and Grubmueller: http://www.mpibpc.gwdg.de/groups/grubmueller/start/people/olange/gencorr.html > > Much thanks, > > Arneh greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
