From: Jérôme Hénin (
Date: Fri Jun 11 2004 - 09:34:45 CDT

Hi John,

I'm using 1.8.2. My mom taught me never to report problems with older versions
of software.

I've heard that the next version of vmd is expected in a (more or less) near
future. But if this is a limit of the basic algorithm itself, I imagine there
is nothing to do to improve it.

Anyway, I'm glad to know this is a known problem. From now on, I'll check for
that kind of behaviour.


Le Vendredi 11 Juin 2004 16:04, John Stone a écrit :
> Hi Jerome,
> Which version of VMD are you using?
> We've had a couple of implementations for the RMS alignment code, so
> knowing which version you're using would tell me which alignment code was
> in use. The older versions performed less well than the newest version.
> However, that said, I also believe there there are numerical circumstances
> that can cause many of the implementations derived from the Kabsch
> algorithm to fail to converge within a reasonable number of iterations,
> which may explain why yours worked on the second attempt. I have seen some
> structures that don't align well even with repeated attempts.
> John
> On Fri, Jun 11, 2004 at 09:48:49AM +0200, Jérôme Hénin wrote:
> > Hi all,
> >
> > I have met an unexpected behaviour using the "measure fit" command, and
> > I'd like to know if anyone has had a similar experience.
> >
> > When computing the rmsd along a trajectory, some frames were not properly
> > aligned with the reference system, which resulted in jumps in the
> > measured rmsd. By repeating the fitting procedure, the alignement problem
> > was eventually corrected.
> >
> > Is this to be considered a bug of the alignement algorithm?
> >
> > Jerome

Jérôme Hénin
Equipe Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS    UMR 7565
B.P. 239	54506 Vandoeuvre-lès-Nancy Cedex
Tel : (33) 3 83 68 43 95	Fax : (33) 3 83 68 43 71