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

Shirley Siu siu at mpi-sb.mpg.de
Tue Mar 15 19:11:42 CET 2005

Dear Konrad,

The chain is a short peptide chain (only 2 residues) in a big binding
groove, so the sidechains are moving quite much in the simulation.

It look suspicious because I use VMD (by running a tcl script) to
calculate the RMSD of the same chain over the trajectory (which use the
similar approach: fitting the structure to the reference structure, and
then calculate), that give me a very different result: range from 0 to
1.55. The shapes of the curves are also different. Any idea?

By the way, is the RMSD in MMTK using "Ang" as unit?


On Tue, 15 Mar 2005 khinsen at cea.fr wrote:

> 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.
> --
> ---------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------

More information about the mmtk mailing list