Dear Gromacs Users !
I am using gmx_covar to perform PCA of the molecular dynamics trajectory, in order to compute cross-correlation maps of the atomic fluctuations from the covariance matrix.
gmx covar -s ${reference} -n ${ndx} -f ${trajectory} \
-o "${pca_project}"/eigenval.xvg -av "${pca_project}"/averaged_structure.pdb \
-v "${pca_project}"/eigenvect.trr -xpma "${pca_project}"/covarmap.xpm
gmx xpm2ps -f "${pca_project}"/covarmap.xpm \
-o "${pca_project}"/covara_"${project}".eps -rainbow ${pc_bgcolor} \
-nice 900 -title none
how the information from the covariance charts could be related to the cross-correlations?
otherwise would it be possible to get the dynamic cross-correlation maps directly from the covariance maps ? Previously I saw a special version of the gmx covar in the user contribution page that could produce the both outputs but I don’t see it anymore .
Many thanks in advance
Kind regards
James