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.
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 In message <[EMAIL PROTECTED]> Discussion list for GROMACS users <[email protected]> writes: > Samantha Kaye wrote: > > I tried to generate my continuation file from 4500 using tpbconv. Any > > reason the shouldn't work? Do I need to truncate the trr file specifically? > > > if you don't have velocities it won't work. try 4000, or check first > where you do have velocities using gmxcheck. > > > > > > > > In message <[EMAIL PROTECTED]> Discussion list for GROMACS users > > <[email protected]> writes: > >> Samantha Kaye wrote: > >>> But the first file can't be successfully gmxcheck-ed, I get the precision > >>> error mentioned below. > >> ok, I see. You will have to truncate it after 4500 ps using trjconv -e > >> or trjconv -trunc > >> > >>> > >>> In message <[EMAIL PROTECTED]> Discussion list for GROMACS users > >>> <[email protected]> writes: > >>> > >>>> Samantha Kaye wrote: > >>>> > >>>>> Yes using trjcat. It returns a magic number error. > >>>> could this by chance be run on a 64 bit powerpc? > >>>> > >>>> If the two original files can be gmxcheck-ed then the catted file should > >>>> be fine too. > >>>> > >>>> > >>>>> In message <[EMAIL PROTECTED]> Discussion list for GROMACS users > >>>>> <[email protected]> writes: > >>>>> > >>>>> > >>>>>> Samantha Kaye wrote: > >>>>>> > >>>>>> > >>>>>>> Hi, > >>>>>>> > >>>>>>> Whenever I try to make a continuation file for my simulation I can > >>>>>>> generate a tpr file using tpbconv but I can't cat the ouput files > >>>>>>> together afterwards. > >>>>>>> > >>>>>> did you use trjcat ? > >>>>>> > >>>>>> > >>>>>> > >>>>>>> When I run ">gmxcheck -f closed1122_unrest.trr" on the first trr file > >>>>>>> I get the following: > >>>>>>> > >>>>>>> > >>>>>>> Checking file closed1122_unrest.trr > >>>>>>> trn version: GMX_trn_file (single precision) > >>>>>>> Reading frame 0 time 0.000 > >>>>>>> # Atoms 189376 > >>>>>>> Reading frame 910 time 4550.000 > >>>>>>> ------------------------------------------------------- > >>>>>>> Program gmxcheck, VERSION 3.3 > >>>>>>> Source code file: trnio.c, line: 66 > >>>>>>> > >>>>>>> File input/output error: > >>>>>>> Can not determine precision of trn file > >>>>>>> ------------------------------------------------------- > >>>>>>> > >>>>>>> > >>>>>>> I've tried generating the continuation file from an earlier frame but > >>>>>>> have the same problem always at frame 910. > >>>>>>> > >>>>>>> The file is over 2gb but as tpbconv runs without a problem I don't > >>>>>>> think that's the problem. > >>>>>>> > >>>>>>> Any suggestions? > >>>>>>> > >>>>>>> Thanks > >>>>>>> > >>>>>> > >>>>>> -- > >>>>>> 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 > >>>> > >>> > >> > >> -- > >> 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
