[gmx-users] Cross correlation map of residues

[Florent Hédin]

Hi,

In case you really want to produce something similar, I have a solution 
( 2 in fact ;-) )

This plot is easy to produce with the R package bio3d, unfortunately it 
only supports charmm/namd dcd and amber ncdf trajectory types.

The first option : would be to use vmd for converting a gmx trajectory 
to, for example, dcd. Then follow the bio3d tutorials of R.

The second option is : R is really modular, you can write a piece of C 
code reading the gromacs trajectory and returning it (frame by frame) to 
R. This code is compiled as a shared library, and in R you would just 
easily load it. I already have some code doing that, if interested I can 
share it. On long term I plan to put this piece of code directly into a 
R package.

Regards,

Florent Hédin

On 03/06/16 08:02, Tsjerk Wassenaar wrote:
> 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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>
>
>