About RMSD calculation.

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Fri Oct 28 2005 - 10:49:14 CDT

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 Wang,
Email - bwang9_at_uic.edu
Major - Phys. Chem.
dept Chemistry,
Univ Illinois, Chicago,
60607 IL US.

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