Dear developers,
First, thanks a lot for all your efforts. I am writing to ask if it is possible to add a small feature to gmx cluster, which is the possibility to write the full RMSD matrix in a file that could be read by Numpy. I am aware of the -nlevels flag, but what I need is the full matrix with more resolution.
The reason is the following: we have developed a new clustering algorithm, which outperforms existing algorithms in several applications including simulations of biomolecules (and moreover, it is easier to use and understand than many methods). As many clustering algorithms, we need a pair-wise distance matrix and what we are currently doing is computing with gromacs the RMSD with respect to each frame and then concatenate everything to a single file. It works, but is tedious. Since the distance matrix is computed by gmx cluster, I was thinking that it shouldn’t be too complicated to output it in a file, but many I am wrong and missing something.
Thanks a lot in advance. And of course, I am available if you need more details.
Nicolas
PS: We plan to submit the paper in January in case you are interested in the method.