From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 11 2008 - 00:48:35 CDT

Axel,
  I just looked at the CVS revisions for the LAAMMPS plugin
and VMD 1.8.6 already includes the version that avoided
using atom indices as names. My guess is that this problem
was caused by one of the other free-form formats like .xyz,
perhaps outputted by custom software or something, we'll see
what Alexandre says.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 10, 2008 at 11:19:36AM -0400, Axel Kohlmeyer wrote:
> On Sat, 10 May 2008, John Stone wrote:
>
> JS>
> JS> Hi,
> JS> What file format did you load your structure from?
>
> john,
>
> that reminds me. the LAMMPS molfile plugin used to have the
> stupid behavior of assigning the atom number as atom type
> (and waste an insane amount of memory because of that, too).
> is the fix that we integrated quite a while ago in 1.8.6 or
> was it after the release? that could be the reason...
>
> cheers,
> axel.
>
> JS> The message you're getting from VMD isn't about the number of atoms,
> JS> it's about the number of unique atom nams, types, residue names,
> JS> segment names, chains, or alternate location identifiers. Normally
> JS> you would never encounter this error message unless you did something
> JS> such as giving every atom in your system a unique name (which will
> JS> also cause other problems since VMD probably won't recognize the atom names)
> JS>
> JS> We regularly work with multi-million atom structures with VMD, so if
> JS> you specify your structure in a reasonable way there shouldn't be
> JS> any problem.
> JS>
> JS> Cheers,
> JS> John Stone
> JS> vmd_at_ks.uiuc.edu
> JS>
> JS> On Sat, May 10, 2008 at 05:36:43PM +0500, Alexandre A. Vakhrouchev wrote:
> JS> > Hi all!
> JS> >
> JS> > I've got such message working with 2000K atom system. Is there any
> JS> > other approaches to solve that for VMD 1.8.6? Just now I had to
> JS> > downgrade to 1.8.5 for quick solution.
> JS> > --
> JS> > Best regards,
> JS> >
> JS> > Dr. Alexander Vakhrushev
> JS> > Institute of Applied Mechanics
> JS> > Dep. of Mech. and Phys.-Chem.
> JS> > of heterogeneous mediums
> JS> > UB of Russian Academy of Sciences
> JS> > 34 T. Baramzinoy St.
> JS> > Izhevsk, Russia 426067
> JS> >
> JS> >
> JS> >
> JS> > --
> JS> > Best regards,
> JS> >
> JS> > Dr. Alexander Vakhrushev
> JS> > Institute of Applied Mechanics
> JS> > Dep. of Mech. and Phys.-Chem.
> JS> > of heterogeneous mediums
> JS> > UB of Russian Academy of Sciences
> JS> > 34 T. Baramzinoy St.
> JS> > Izhevsk, Russia 426067
> JS> > ----------------------------------
> JS> > ,
> JS> >
> JS> >
> JS> > ..-.., ...
> JS> >
> JS> >
> JS> >
> JS> > 426067, .
> JS> > . . 34
> JS> > +7(3412)21-45-83
> JS>
> JS>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.

-- 
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