<p>Hi Udi,</p>
<p>Square the numbers... It's Root Mean Square Deviation, right? But roots don't add up like that.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Aug 12, 2010 12:02 AM, "udi" <<a href="mailto:udi_zel@012.net.il">udi_zel@012.net.il</a>> wrote:<br><br>
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Hi gromacs users,</p>
<p class="MsoNormal">I’m simulating a protein that consists of 5 domains. I
have calculated the whole protein’s backbone RMSD by entering ‘4’
twice.</p>
<p class="MsoNormal">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.</p>
<p class="MsoNormal">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? </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thanks from advanced</p>
<p class="MsoNormal">Chears</p>
<p class="MsoNormal"> </p><font color="#888888">
<p class="MsoNormal">Udi </p>
</font></div>
</div>
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