From: Michael Morgan (
Date: Fri Aug 14 2020 - 17:31:09 CDT

Dear friends,


Recently I calculated RMSD for a system (including DNA and protein) using
charmm and VMD respectively. Three RMSDs were calculated: DNA alone, protein
alone, and everything altogether (DNA+protein). Surprisingly, I got quite
different numbers for DNA RMSD, while quite good agreements for the RMSDs of
protein and everything. The trajectory file contains 5000 frames, and all
5000 ratio numbers for rmsd(charmm)/rmsd(vmd) are within 0.997-1.014
(average 1.00) for protein. For everything, it is 0.96-1.02 (average 0.998).
However, for DNA, it is 0.5-1.0 (average 0.87)! The shapes of the RMSD plot
of DNA are quite similar though. It seems to me that there is a different
weight factor for the plot. However, I don't understand why it does not
affect protein and everything plot. Any suggestions about what I might miss?


Btw, the RMSDs were calculated without H and aligned with protein first.


Thank you very much.