VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 29 2008 - 12:39:20 CST

Hi,
  Yes, you'll either have to unwrap your coordinates from PBC
or else keep them all within the unit cell with no boundary crossings
in order to get successfull alignments. If pieces of the structure
cross the PBC cell boundaries, the alignment algorithm will not work.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 29, 2008 at 07:15:49PM +0100, Jorgen Simonsen wrote:
> Hi,
>
> sorry for the few information. I loadede my peptide along with the *dcd file
> into VMD with 8500 frames when I look at the file - the peptide is moving
> forth and back once in a while due to periodic boundary conditions. In order
> to compute the rmsd I first want to align the peptide - I use the
> align-method which is within VMD in the RMSD Trajectory Tool. If I f.ex.
> remove the first 1000 frames I only get 8 of these warning...
> Could it be due to the jumps from the PBC? Should I remove these for my
> computation. Thanks in advance and sorry for the few info..
>
> Best,
>
>
> On Fri, Feb 29, 2008 at 6:07 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > The convergence warning occurs when the alignment algorithm
> > (which uses an iterative solver) cannot reduce the residual
> > numerical error below a predefined tolerance. You could get
> > this sort of thing when operating on ill-conditioned data resulting
> > from structures or trajectory frames that don't match very well.
> > In VMD 1.8.6 we made the alignment criteria more strict, so
> > these messages will likely become more common.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Feb 29, 2008 at 12:00:10PM -0500, weilin Zhang wrote:
> > > Hi John
> > >
> > > I have the same problem.
> > > It is a 10 residue peptide in vmd 1.8.6 on linux..
> > > I am using RMSD trajectory tool and trying to align with top.
> > > Such warnings happens but alignment looks fine.
> > > I am also curious about such information. What is reason for that?
> > >
> > >
> > > Best
> > >
> > > Weilin
> > >
> > >
> > > John Stone wrote:
> > > >I would say that there's something amiss with the structures that
> > > >you're attempting to align. You're actually the first person that
> > > >I'm aware of that has ever gotten the "no convergence" warning.
> > > >
> > > >Can you check to make sure that the atom indices match up between the
> > > >two structures? If they do not, that might cause this sort of problem.
> > > >
> > > >Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > >On Fri, Feb 29, 2008 at 02:03:18PM +0100, Jorgen Simonsen wrote:
> > > >
> > > >>Hi all,
> > > >>
> > > >>I am aligning a small protein 60 residues but when I try to align
> > either
> > > >>using a script or within VMD I get the following error
> > > >>
> > > >>vmd > Matrix: Warning: no convergence (0.00001000<2471.54272461 after
> > > >>1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2621.95825195 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2537.53881836 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2660.39746094 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2565.06079102 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2603.86938477 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2722.60668945 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2739.83642578 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2781.16186523 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2830.56494141 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2861.32617188 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2903.87231445 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2882.46435547 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2583.71997070 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2723.31542969 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<3037.93212891 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2877.39111328 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2822.49243164 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<3063.49023438 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2614.22607422 after 1000
> > > >>iterations).
> > > >> Matrix: Warning: no convergence (0.00001000<2570.64282227 after 1000
> > > >>iterations).
> > > >>
> > > >>how to fix this? Any advice or suggestions appreciated
> > > >>
> > > >>Thanks in advance
> > > >>
> > > >
> > > >
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> > 

-- 
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