VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 04 2006 - 10:38:26 CDT

Lubos,
  I did another test this morning and fixed an uninitialized variable in
the DLPOLY history reader plugin which was the likely cause of the problem
you were having (since you weren't skipping timesteps). Needless to say,
it was a rather important variable. :-) The plugin was working on platforms
that habitually initialize allocated memory to zeros, but had a good chance
of failing on those that do not. Anyway, I think this ought to cure the
crashing you observed, and I've posted freshly built plugins in the same
place on biocore for you and anyone else that's using DLPOLY with VMD:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 04, 2006 at 08:28:45AM -0500, John Stone wrote:
>
> Lubos,
> Argh, I forgot to increase the version number of the dlpoly plugin when
> I fixed the bug the other day, and so VMD isn't picking up the new .so file
> (it's using the statically linked plugin still) yet. Let me build you
> another one and hopefully that'll do it.
>
> John
>
> On Thu, May 04, 2006 at 08:09:54AM +0200, Mgr. Lubos Vrbka wrote:
> > john,
> >
> > > I've posted a set of current plugins I just built in the VMD Public area on
> > > BioCoRE (in the "plugins" subdirectory):
> > > http://www.ks.uiuc.edu/Research/vmd/alpha/
> > >
> > > You'll find plugins for all of the platforms in there. Try the updated
> > > dlpoly plugin in:
> > > LINUXAMD64/molfile/dlpolyplugin.so
> > i downloaded the plugin, replaced the old version with it, but i still
> > get segfaults immediately when loading dlpoly history files (either with
> > 1 frame or real trajectories). the only message i get is 'segmentation
> > fault'.
> >
> > is there any way how i can help you to debug the problem?
> >
> > regards,
> > lubos
> >
> > --
> > .....................................................
> > Mgr. Lubos Vrbka
> >
> > Center for Biomolecules and Complex Molecular Systems
> > Institute of Organic Chemistry and Biochemistry
> > Academy of Sciences of the Czech Republic
> > Prague, Czech Republic
> >
> > http://www.molecular.cz/~vrbka
> > .....................................................
>
>
>
> --
> 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 

-- 
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