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

bipin singh bipinelmat at gmail.com
Sat Jul 18 07:32:32 CEST 2015

There is a modified version of g_covar available at the below link for
calculating correlation matrix:



Thanks and Regards,
Bipin Singh

On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian <m.ebert at umontreal.ca>

> 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,
> max
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