[gmx-users] trajectory file problem

Bert de Groot bgroot at gwdg.de
Mon Jan 27 13:50:11 CET 2003

Luciane Vieira de Mello wrote:
> Hi David
> Thanks for the mail.  gmxcheck stops at the same point 1.9ns into either
> the xtc or trr files.
> There are indeed problems in the /var/log/messages file.  A large number
> like this
> Jan 27 10:00:56 bemtevi kernel: hda: dma_intr: status=0x51 { DriveReady
> SeekComplete Error }
> Jan 27 10:00:56 bemtevi kernel: hda: dma_intr: error=0x40 {
> UncorrectableError }, LBAsect=98790130, sector=78210864
> Jan 27 10:00:56 bemtevi kernel: end_request: I/O error, dev 03:03 (hda),
> sector 78210864
> What does this mean?  A hardware error?  

looks like it...

> If that were the case, it's a big
> coincidence that both trr and xtc have problems 1.9 ns in!  

not if they were written at the same time (by mdrun)

>Could ngmx
> have crashed at that point while reading both files and left problems of
> this kind?  

seems improbable. ngmx can't have opened both .trr and .xtc simultaneously?

> I don't want to rush to blame gromacs but if this is possible
> then it's a very serious (potential) bug.

was there an error like the abovementioned one the time that you ran ngmx OR 
when mdrun wrote the .trr and .xtc files (at 1.9 ns)?


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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