From: Iman Salehinia (isalehinia_at_gmail.com)
Date: Mon Jan 26 2009 - 16:10:39 CST

Dear John,

Thank you for your remarks. The problem is that my friend can not remember
exact number of atoms and how large that file was!
As I told Axel, he was using LAMMPS. The output file was a dcd or xyz file.
Now you have assured me that it works even for 150 million atoms. Thank you.

Regards,
Iman.

On Mon, Jan 26, 2009 at 1:42 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Iman,
> I've loaded systems containing up to 150 million atoms, so believe me,
> there's no serious limitation in the VMD code itself in regards to working
> with large models. You didn't specify anywhere near enough information
> about the problem to allow anyone to help you effectively.
>
> I haven't seen any replies since Axel asked you whether you're using LAMMPS
> or not. That'd be worth noting since an early version of the LAMMPS
> plugin for VMD had some shortcomings that might explain the problem
> your friend has encountered, but still, in order for anyone to provide
> assistance, you need to provide a concrete example of the problem you're
> having (along with files, VMD saved state, etc).
>
> Finally: it's good mailing list etiquette to create a new subject line
> rather than posting by replying to a completely unrelated email
> without changing the subject line.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 22, 2009 at 04:21:59PM -0800, Iman Salehinia wrote:
> > Dear John,
> >
> > One of my friends using VMD had a problem for his modeling. The number of
> > atoms in his model is about 1000000 and VMD didn't work with this amount
> of
> > atoms (his memory is 4 GB). Will this problem be solved in the new
> version
> > of VMD? AtomEye doesn't have this problem, so this problem really forces
> > anyone to not to work with VMD, actually when the number of atoms is big!
> >
> > Regards,
> > Iman.
> >
> > On Thu, Jan 22, 2009 at 9:33 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > >
> > > Hi,
> > > These aren't accessible via the scripting interface in existing
> > > versions of VMD, because VMD versions 1.8.6 and earlier did not
> > > store this information internally. The next version of VMD,
> > > version 1.8.7 (currently in development), stores this information,
> > > and will add new query routines for this purpose. I haven't yet added
> > > the query routines but will let you know when this feature has been
> > > added to a test version. I'm completing the upgrade to Tcl 8.5.x at
> > > present, and will likely add the new query routines for
> > > angles/dihedrals/etc
> > > shortly thereafter.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Wed, Jan 21, 2009 at 04:29:54PM -0500, Maxim Paliy wrote:
> > > > Dear VMD experts
> > > > I want to access the lists of bonds angles dihedrals etc,
> > > > i.e. the information normally contained in the PSF file,
> > > > after the PSF file has been read into VMD.
> > > >
> > > > Sorry if this question is dumb, but I cannot find
> > > > what variables all these data are stored in..
> > > >
> > > > Thanks a lot in advance for any suggestions,
> > > > Maxim
> > >
> > > --
> > > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>