[gmx-users] Cross-correlation map of protein residues

Ebert Maximilian m.ebert at umontreal.ca
Fri Jul 17 16:50:54 CEST 2015

Dear list,

I am looking for a gromacs tool which is able to calculate/draw a map of residues which are either in their motion correlated or anti correlated. first i thought i could just use g_covar with c-alpha and use the -xpma option but while reading previous mailing list posts people said that the atomic covariance matrix does not correlate motions. All posts I found where older and the script from the gromacs site for a g_covar tool which can calculate the correlation plot is from 2009. Therefore, i wanted to know if gromacs 5 is able to directly calculate the plot. if not does anybody know a straight forward way of doing so for a gromacs trajectory?

thank you very much,


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