[gmx-users] Cross correlation map of residues

[Florent Hédin]

Hi,

I now realise that I forgot to ask something essential: do you want to 
perform this normal mode analysis cross correlation map on just one 
pdb/gro coordinates file, on on a full gromacs trajectory ?

Here is an example performing the nma-ccm analysis for one pdb file :

https://gist.github.com/FHedin/07e07e3fe695a15a002850a2e44a2df9

For documentation see :

http://thegrantlab.org/bio3d/html/dccm.nma.html

If you want to perform a dynamic cross correlation map using a 
trajectory file see:

http://thegrantlab.org/bio3d/html/dccm.xyz.html

Regards,

Florent

On 03/06/16 12:00, Qasim Pars wrote:
> Hi,
>
> @Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
> Unfortunately this tool generates the colorless correlation matrix (.xpm)
> on atoms. Whereas I would like to have the colourful correlation matrix on
> residues (not based on atoms). I think there is no way to get the colourful
> correlation matrix on residues by g_correlation tool?
>
> @Florent: The R package bio3d is complex :( It would be good if you share
> on the user list such a code to generate the correlation matrix?
>
> Cheers,
>
> On 3 June 2016 at 11:27, Florent Hédin <work at fhedin.com> wrote:
>
>> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>