[gmx-users] g_rms question

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 12 09:23:05 CEST 2010

Hi Udi,

Square the numbers... It's Root Mean Square Deviation, right? But roots
don't add up like that.



On Aug 12, 2010 12:02 AM, "udi" <udi_zel at 012.net.il> wrote:

 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

Thanks from advanced



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