[gmx-users] RMSD and RMSF
Mark.Abraham at anu.edu.au
Wed Dec 21 03:04:19 CET 2005
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.
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