[gmx-users] Cross correlation map of residues

[Tsjerk Wassenaar]

Hi Qasim,

The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars <qasimpars at gmail.com> wrote:

> Dear gmx users,
>
> I need to get the cross correlation map of all residues belonging to a
> protein (like this figure
> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
> ).
> Is there any tool to get such a plot with GROMACS?
>
> By the way, gmx covar -xpma gives the cross correlation for each atom pair
> but it is not what I want.
>
> Any suggestions will be appreciated.
>
> --
> Qasim Pars
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-- 
Tsjerk A. Wassenaar, Ph.D.