VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 03 2009 - 16:18:43 CST

Bob,
  VMD currently uses a very small tolerance parameter for the
RMS fit routine to encourage complete convergence in some
difficult corner cases. In your case, even after 1,000 iterations
the algorithm's convergence criteria hasn't been entirely satisfied
given the tiny tolerance we've allowed by default, but that said,
it may not be possible for yours to align any better than they are.
For now, I'd consider this to be only a warning for your cases,
and not something to worry about. I'm looking at another approach
for improving the touchy cases without making the convergence test
tolerance parameter so unrealistically tight.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 03, 2009 at 03:49:29PM -0500, Bob Johnson wrote:
> Hello everyone,
> I have a script that simply fits a reference structure to the
> instantaneous protein structure (using 'measure fit') and then
> computes the RMSD. For some of the frames, an error is generated that
> states "Matrix: Warning: no convergence (0.00000000<390.26229858 after
> 1000 iterations)." What is causing this error? It seems that, overall,
> the two structures are fitted correctly. I'm not sure why certain
> frames are problematic.
> Thanks,
> Bob
>
> --
> Bob Johnson, PhD
> Institute for Computational Molecular Science
> Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> http://www.sas.upenn.edu/~robertjo 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078