I've performed a MD simulation for a protein using GROMACS, and I want to obtain a map for the generalized correlation/dynamic cross correlation in relation to this protein. Note that I'm not sure at this moment if these terms are synonyms.
I already know how to construct the covariance matrix using the gmx covar. Now I'm not sure how I should proceed. It seems that I can use the program g_correlation (available in this page: https://www.mpibpc.mpg.de/grubmueller/g_correlation) to obtain the generalized correlation matrix from the covariance matrix. However, I couldn't find any information on how to use it.
It seems that VMD (1.9.3) has a cross-correlation program inside the Timeline. However, it requires a Density Map file that I don't know exactly what it is. I tried to calculate it using the MapTool on VMD, but it didn't work out.
So, any ideas on how to obtain the correlation maps using these or any other programs are welcome.
This is not GROMACS, but I do simulations using the AMBER force field with CHARMM DCD as output using NAMD. The AMBER suite has a program called cpptraj for trajectory analyses. This program conveniently handles matrix correlation analysis.
g_correlation is a very nice tool for this purpose. Supply it a tpr file, xtc file and an index file if you have specific sub-groups you want to analyze. Or you can just do a complete C-alpha correlation map. It dumps an xpm file which you can further visualize. You need to install gromacs 3.3 with older version of fftw and then you can install g_correlation. if you face issues with installation let me know. Some header files might need some correction. Good luck
Thank you for your answer, Sarath!
The first step, then, is to install g_correlation. I believe I can easily install GROMACS 3.3. The question now is: What specifically is this "older version" of FFTW that I need? I ask it because I remember that in some older versions of GROMACS the automatic installation of FFTW wouldn't work sometimes, so I had to do it manually. If this is the case, I have to know exactly the version of FFTW I'm looking for (unless it's obvious).
This is not GROMACS, but I do simulations using the AMBER force field with CHARMM DCD as output using NAMD. The AMBER suite has a program called cpptraj for trajectory analyses. This program conveniently handles matrix correlation analysis.
Hi Adam,
Thanks for your answer!
It's good know, specially for those with access to AmberTools. I did a check here, and it seems that cpptraj can read some of the GROMACS trajectory files, though it doesn't seem to be able to read the trajectory file I'm using (.xtc). So, one could indeed use AmberTools to do these analysis. However, since all my trajectories are in .xtc and I don't have access to AmberTools, it's not an option for me.
Hi Gustavo,
Current versions of fftw3x were not compatible. So I installed fftw215.
If you wish to run g_correlation in parallel, you will need lamboot. I had tough time finding the source. You can download it using the following link (https://drive.google.com/file/d/0B5Dd3UBjK1BPd2RGZUJIZGZpSnM/view?usp=sharing) I hope you will find it useful. Good luck.
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