VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 25 2009 - 07:41:11 CDT

Hi,
  Are you running out of memory on your machine?
That's what it looks like to me from the errors you're getting.

A second issue here is that you've got 12 million atoms, which goes
beyond the limits of the normal PSF file format. We have built
structures this large, but we had to use our own file formats rather
than PSF/PDB because various field widths overflow with the standard
PSF/PDB files. What do you plan to do with the system next? If you're
going to simulate with NAMD, you'll have to do what we've been doing
and use the other file formats. I have special builds of VMD and psfgen
that can emit files in the other formats for setting up huge simulations
like this.

If you tell us more about what you're attempting to do,
I can either provide you with the needed VMD/psfgen builds that enable
output to the .js file format or give you alternative suggestions.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Fri, Sep 25, 2009 at 12:40:17PM +0200, Luca Gelisio wrote:
> Hi to all,
>
> I'm building a huge Solvation Box (500x500x500), rotating water molecules.
> When VMD finishes building I get the following error followed by a
> segmentation fault:
>
> ERROR) Error reading bond information.
> Segmentation fault
>
> Here the whole output, from last generated segment:
>
> building segment W511
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> building segment W512
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> Info: writing psf file solvate.psf
> total of 12337020 atoms
> total of 8224680 bonds
> total of 4112340 angles
> total of 0 dihedrals
> total of 0 impropers
> total of 0 cross-terms
> Info: psf file complete.
> Info: writing pdb file solvate.pdb
> Info: pdb file complete.
> clearing structure, preserving topology and aliases
> Info) Using plugin psf for structure file solvate.psf
> ERROR) Error reading bond information.
> Segmentation fault
>
> Can this error be avoided?
>
> Many thanks,
>
> luca 

-- 
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