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 <[EMAIL PROTECTED]> Discussion list for GROMACS users <[email protected]> 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 <[EMAIL PROTECTED]> Discussion list for GROMACS users > > <[email protected]> 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 > >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 [EMAIL PROTECTED] > >> 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Samantha Kaye Structural Bioinformatics and Computational Biochemistry Group University of Oxford _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
