[gmx-users] trajectory file problem

[Bert de Groot]

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)?

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________