VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Mon Jun 12 2006 - 14:10:19 CDT

Sure, will do, thanks!

John Stone wrote:
> 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]$
>>
>
>