[MMTK] calculate RMSD of a collection of atoms from trajectory

khinsen at cea.fr khinsen at cea.fr
Tue Mar 15 18:56:59 CET 2005

On Mar 15, 2005, at 18:49, Shirley Siu wrote:

> I would like to calculate the RMSD of some atoms from the trajectory,
> using the first frame as the reference. However, the result showed only
> very little different and it is suspicious. I wonder if my way of
> doing it is correct or not.

It looks correct, as do the numbers, assuming your trajectory 
represents protein dynamics rather than some big-scale event such as 
folding or unfolding. What kind of values were you expecting?

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr

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