VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Aug 15 2020 - 20:30:19 CDT

Dear Michael,
It would be helpful for you to give the exact procedures (including
commands) that you used in both cases, so that others can see and replicate
the exact procedure that lead to the behavior that you observed.
Best,
Peter

On Fri, Aug 14, 2020 at 8:23 PM Michael Morgan <michaelmorgan937_at_gmail.com>
wrote:

> 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.
>
>
>
> Michael
>
>
>