AMBER Archive (2004)

Subject: AMBER: Question about RMSD calculation

From: yonchen (
Date: Wed Mar 03 2004 - 22:25:01 CST

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:

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

Thanks a lot.

Best Regards
Yongzhi Chen

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