VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Mon Jun 12 2006 - 11:47:06 CDT

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]$