VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 12 2006 - 13:42:26 CDT

Arneh,
  We fixed a bug in the gromacs related plugins before the final
release of VMD 1.8.4. Can you try upgrading to VMD 1.8.4 and re-try?

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 12, 2006 at 09:47:06AM -0700, Arneh Babakhani wrote:
> Hi all,
>
> I get a 'segmentation fault' (see below) when I try to load up a GROMACS
> trajecotry. I'm only getting this error with one particular trajectory
> (others load up just fine). Does that mean there's a problem with my
> trajecotry file? (there was no indication from GROMACS that that's the
> case, it seemed to run fine). Or am I missing something in VMD?
>
> Thanks,
>
> Arneh
>
> -----------
> [ababakha_at_chelinuxtest Minimization]$ vmd -dispdev text
> AfterEMSteep-froz.gro CGMin-froz.trr
> Info) VMD for LINUX, version 1.8.4b11 (February 10, 2006)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 1 CPU detected.
> Info) File loading in progress, please wait.
> Info) Using plugin gro for structure file AfterEMSteep-froz.gro
> Info) Using plugin gro for coordinates from file AfterEMSteep-froz.gro
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file AfterEMSteep-froz.gro.
> Info) Analyzing structure ...
> Info) Atoms: 25925
> Info) Bonds: 19168
> Info) Residues: 6775
> Info) Waters: 6631
> Warning) Unusual bond between residues: 1 (none) and 2 (protein)
> Warning) Unusual bond between residues: 7 (protein) and 8 (none)
> Warning) Unusual bond between residues: 9 (none) and 10 (protein)
> Warning) Unusual bond between residues: 15 (protein) and 16 (none)
> Info) Segments: 1
> Info) Fragments: 6761 Protein: 2 Nucleic: 0
> Info) Using plugin trr for coordinates from file CGMin-froz.trr
> Segmentation fault
> [ababakha_at_chelinuxtest Minimization]$ 

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