VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 26 2009 - 15:42:17 CST

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/      Fax: 217-244-6078