VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat May 10 2008 - 10:19:36 CDT

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> > ----------------------------------
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JS> >
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JS> > 426067, Ç. éÖÅ×ÓË
JS> > ÕÌ. ô. âÁÒÁÍÚÉÎÏÊ 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.