Re: rmsd colvar

From: Giacomo Fiorin (
Date: Mon Nov 02 2020 - 08:57:31 CST

Hi Stefano, most often the RMSD of a protein or a protein domain is defined
by including the rotation + translation that minimizes i.e., the best-fit
alignment against the reference coordinates. In the RMSD implementation
provided by Colvars, this alignment is computed by default on the same
atoms on which the RMSD is defined:
and you shouldn't need to apply restraints to prevent drift: the RMSD will
be expressed in the moving frame of reference, wherever the protein goes.
You just need to take care that the coordinates of the protein are either
unwrapped, or wrapped together for the whole protein.

You also have other options to fine-tune this:
although using different groups for the best-fit and the RMSD computation
adds extra computation that is otherwise not needed for a standard RMSD.


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