Re: Is it better to align all the trajectory before calculating rmsd?

From: Ana Vila Verde (
Date: Tue Jan 22 2008 - 05:31:12 CST

It makes more sense to first align the protein and then calculate its
RMSD, if your intention is to evaluate its structural stability. It is
legitimate to calculate the RMSD without alignment only when you want to
evaluate the rotation/translation diffusion of the protein (which is a
separate issue of the protein's stability).

Hope it helps,


dongsheng lei wrote:
> Hello!
> In some paper about simulating protein with namd, I find they verify
> the equilibration of protein by the root mean square deviation
> (RMSD).But they don't align all the trajectory before calculating rmsd.
> Is it better to align the entire trajectory to the initial structure
> before calculating the rmsd, for rmsd may be derived from translation
> and rotation?
> Are there some other methods to verify the equilibration of protein?
> Thank you very much!!
> Best wishes

Ana Vila Verde
Post-doctoral scholar
FOM Institute for Atomic and Molecular Physics [AMOLF]
P.O.Box 41883
1009 DB Amsterdam
The Netherlands
Phone: +31-20-6081392
Fax: +31-20-6684106
University of Minho
Physics Center
Campus de Gualtar
4710-057 BRAGA

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