# AMBER: Question about RMSD calculation

From: yonchen <yonchen.ic.sunysb.edu>
Date: Thu, 04 Mar 2004 04:25:01 GMT

Dear Amber community:

Now let me explain my understanding for this definition. When we
consider calculating RMSD of a structure, the numerator term in the
square root is a sum whose inner loop is a sum over time and outer loop
is a sum over space. Then this sum divide the number of atoms include by
this structure.

Now going back to my simple test data:
For t=2 case, RMSD for only residue 1, residue2 and residue 1 to 2 are
0.22, 0.05 and 0.60 respectively. To simplify the model, we treat every
residue as an atom. According the formula, the RMSD for residue 1 to 2
should be less than 0.22. But it is 0.60. Where is my fault?

By the way, I found the definitions of RMSD are different in the
following resource:
http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02
-namd-tutorial/namd-tutorial-html/node11.html#SECTION0002710000000000000
0

http://www.ks.uiuc.edu/Training/SumSchool03/Tutorials/vmd/node4.html#SEC
TION00045000000000000000

Could you tell me where I can find a normal one?

Thanks a lot.

Best Regards
Yongzhi Chen

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Received on Thu Mar 04 2004 - 04:53:01 PST
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