I am going to try but there's a queue on the cluster at the moment so it may take a day or more.


In message <44C5F647.4090505@xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users@gromacs.org> writes:
> Samantha Kaye wrote:
> > The files are over 2gb and I'm using gromacs 3.3 on a linux cluster with amd64's (is that enough info? let me know if you need more).
> > 
> > The only frame info I get is counting through the frames being checked until it gets to the last (corrupt) one at 4550.
> > 
> > Thanks for your help David. It's appreciated.
> > 
> 
> Magic number errors can be caused by flaky hardware or software, e.g. 
> intermittent NFS failures (or temporary full disks) sometimes corrupt 
> files without crashing. Is the 910 ps problem reproducible? You could 
> restart the calculation from the same tpr file and see if the problem 
> reoccurs. Since MD is deterministic it should give the same result.
> 
> 
> > 
> > In message <44C5C7BD.1080109@xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users@gromacs.org> writes:
> >> Samantha Kaye wrote:
> >>> When I tried to cat the results of that continuation file (started from 4500) it also has a magic number error at frame 910 (which is now in the second file) so I will try to truncate my trr file as suggested.
> >>>
> >> did you say what platform this is? are the files larger than 2Gb?
> >>
> >>
> >>> One further question, how do I get gmxcheck to tell me this? I don't get any output other than the error message. Is there a verbose option in there somewhere? At the moment I'm just running gmxcheck -f file.trr 
> >>>
> >> It should say how many frames there are etc. but maybe not if it crashes...
> >>
> >>
> >>
> >>
> >> -- 
> >> David.
> >> ________________________________________________________________________
> >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >> Dept. of Cell and Molecular Biology, Uppsala University.
> >> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> >> phone:	46 18 471 4205		fax: 46 18 511 755
> >> spoel@xray.bmc.uu.se	spoel@gromacs.org   http://folding.bmc.uu.se
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users@gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-request@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> > 
> 
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel@xray.bmc.uu.se	spoel@gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
Samantha Kaye
Structural Bioinformatics and Computational Biochemistry Group
University of Oxford