Hello, I am interested in dynamical analysis of my protein. In the manual, it says -ascii generates a file that includes the whole covariance matrix, and -xpma writes the atomic covariance matrix per pair of atoms. I was wondering if there is a way to have this atomic covariaces in the .dat file with -ascii switch. Otherwise, is there a script in gromacs that converts the xpm to an ascii file? In addition, is the -xpma output normalized? Thanks for your help.
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