From: Luca Gelisio (luca.gelisio_at_gmail.com)
Date: Fri Sep 25 2009 - 09:03:41 CDT

I'm sorry Axel, your absolutely right:

VMD version: 1.8.7 (2009-08-01)
platform: Linux (64-bit x86) with CUDA
specs: Intel i7 CPU 920 @ 2.67GHz, 6Gb RAM + 12 Gb swap, NVIDIA GTX295 +
NVIDIA GTX285, 500Gb HD
OS: Ubuntu Linux 9.04

2009/9/25 Axel Kohlmeyer <akohlmey_at_gmail.com>

> luca,
>
> please always provide information about the version of VMD
> and platform that you are running on. you may well run into
> a problem that has already been solved or that is due to the
> limitations of the platform that you are running. since it will
> take considerable effort to reproduce your problems, it would
> be nice to be able to rule out certain known problems. thanks
>
> ciao,
> axel.
>
> On Fri, Sep 25, 2009 at 6:40 AM, Luca Gelisio <luca.gelisio_at_gmail.com>
> 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
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>