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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

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

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

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

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