VMD-L Mailing List

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Fri Feb 29 2008 - 12:15:49 CST

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
>