Hi gromacs users, I'm simulating a protein that consists of 5 domains. I have calculated the whole protein's backbone RMSD by entering '4' twice.
Now, I would like to calculate the contribution of every domain i.e. if the whole protein's RMSD in the first frame is 1nm, then how is this 1nm distributed between the 5 domains. I have created 5 groups in the index file of the backbone of every domain and calculated the RMSD by first entering '4' in order to fit the whole backbone and entered the domains backbone groups in the second entry. (5 different calculations). The problem is that the values I get from the domains do not add up to the whole backbone RMSD values!!! What am doing wrong? Thanks from advanced Chears Udi
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