[gmx-users] RMSD and RMSF

[Mark Abraham]

Anthony Cruz wrote:
> Hi User:
> I have a little question. There is a value for the RMSD or RMSF that can be 
> use to define a large change (RMSD) or high flexibility, like reference 
> number?? any reference???

There is no magic number here. It is critically system-dependent. The 
same value of RMSD for a 600-residue protein and a 10-residue peptide 
can have two totally different meanings. Neither is there any clear way 
to normalize RMSD for system size, much less system type.

RMSD is exactly that - an average deviation between two structures. 
There are other ways one could define average deviation. In the end, 
whether any of them has any meaning for a given pair of structures is a 
scientific judgement that has to be made in individual cases.

Mark