Re: About RMSD calculation.

From: LEWYN LI (
Date: Fri Oct 28 2005 - 15:30:20 CDT


         In order to calculate the RMSD between two structures, the program
must first do a "best-fit" superposition of the two structures, and only
then can RMSD be determined. So the coordinates of one of the structure
must be changed to superimpose on the other structure, as well as it was

         Hope this helps.


On Fri, 28 Oct 2005, Boyang Wang wrote:

> Hi all. I have a basic question.
> When I load a a.psf file and its .DCD files so that I have the
> trajectory over 3000 frames. If I type "source rmsd.tcl" in the TKcon
> window, the "rmsd.tcl" script is supposed to calculate the rmsd of each
> frame compared to the initial frame.
> After the calculation of rmsd, I have found that the coordinates of
> each frame have been changed. I wonder what they have been changed to
> and why are they changed.
> Thanks a lot for the time.
> Boyang
> Boyang Wang,
> Email -
> Major - Phys. Chem.
> dept Chemistry,
> Univ Illinois, Chicago,
> 60607 IL US.
> ---------------------------------
> ŻG䣭йһʼɧų
> Ż֡Dɱɧ

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