question about RMSD defined in NAMD

From: Boyang Wang (
Date: Sat Dec 02 2006 - 19:46:40 CST

Dear all,

I have a question about how RMSD is defined in the
NAMD tutorial.

>From the equation that defines RMSD of a protein, I
can not understand the meaning of Nt.

For example, if I calculate the RMSD of 10 frames of a
protein saved from the simulation, comparing with the
initial conformation of the protein, the rmsd.tcl will
calculate one RMSD value for each of the 10 frames,
comparing with the initial conformation. In other
words, between any frame and the initial conformation,
there is only one RMSD value, and this value is not
related to the time when these two frames are saved.

Does that mean that Nt=1?

Thanks for your time.


Boyang Wang,
Email -
Major - Phys. Chem.
dept Chemistry,
Univ Illinois, Chicago,
60607 IL US.



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