Re: [gmx-users] Broken trr-file
Mark Abraham wrote: Justin A. Lemkul wrote: Hansjoerg Jerabek wrote: Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time 43500.000 # Atoms 25400 Reading frame 4 time 43520.000 Warning at frame 4: coordinates for atom 21839 are large (3.04738e+35) Warning at frame 4: coordinates for atom 21839 are large (2.16053e+185) --- Program gmxcheck_d, VERSION 4.0.3 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- Is it somehow possible to manually remove the corrupt frame from the binary trr-file? I'm asking this because I can't afford to re-run the simulation, since it would take about 3 weeks. trjconv-b 0 -e 3 You will have to sacrifice everything after frame 3 then (since frame 4 is corrupted). Judging by the timeframe of the simulation, that is probably a substantial amount of data. Perhaps you can restart from a checkpoint file, depending on how often those were written, to collect the rest of your data. ... and next time, plan to save yourself data suitable for a restart every few compute hours or so! There's some general information here, but the detail was written for GROMACS 3.3.x. http://wiki.gromacs.org/index.php/Doing_Restarts Mark ... thank you for your advices. since it was impossible to edit the trr-file with any of the gromacs application, I used a hex-editor and a small c++-application to cut the broken frames out. best regards hansjoerg ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Broken trr-file
Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time 43500.000 # Atoms 25400 Reading frame 4 time 43520.000 Warning at frame 4: coordinates for atom 21839 are large (3.04738e+35) Warning at frame 4: coordinates for atom 21839 are large (2.16053e+185) --- Program gmxcheck_d, VERSION 4.0.3 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- Is it somehow possible to manually remove the corrupt frame from the binary trr-file? I'm asking this because I can't afford to re-run the simulation, since it would take about 3 weeks. Best regards Hansjoerg Jerabek Mark Abraham wrote: Hansjoerg Jerabek wrote: Dear colleagues! I faced a problem while trying to modify a trr-file using trjconv_d: trjconv_d -f ketamine.t2.trr -s ketamine.2.tpr -n bilayer.ndx -o ketamine.2.trr -b 43550 In my case the first frame of the trr-file starts at 43500ps (time step: 5ps). I get the following ouput: Will write trr: Trajectory in portable xdr format Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision) Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision) Select group for output Group 0 ( System) has 25400 elements Group 1 (POPC) has 10400 elements Group 2 ( SOL) has 15000 elements Select a group: 0 Selected 0: 'System' trn version: GMX_trn_file (double precision) *Skipping frame 4 time 43520.000 * --- Program trjconv_d, VERSION 4.0.3 Source code file: trnio.c, line: 66 *File input/output error: Can not determine precision of trn file* --- It seems that the 4th frame at 43520ps is broken, but I somehow can't get rid of it. Assuming your file system isn't full or some such, the most likely problem is that the file was garbled when it was written. Check the log file for correct completion, and see what gmxcheck and/or gmxdump have to say about the .trr file. If the file's not been written correctly, there's nothing to do but re-run. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Broken trr-file
Dear colleagues! I faced a problem while trying to modify a trr-file using trjconv_d: trjconv_d -f ketamine.t2.trr -s ketamine.2.tpr -n bilayer.ndx -o ketamine.2.trr -b 43550 In my case the first frame of the trr-file starts at 43500ps (time step: 5ps). I get the following ouput: Will write trr: Trajectory in portable xdr format Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision) Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision) Select group for output Group 0 ( System) has 25400 elements Group 1 (POPC) has 10400 elements Group 2 ( SOL) has 15000 elements Select a group: 0 Selected 0: 'System' trn version: GMX_trn_file (double precision) *Skipping frame 4 time 43520.000 * --- Program trjconv_d, VERSION 4.0.3 Source code file: trnio.c, line: 66 *File input/output error: Can not determine precision of trn file* --- It seems that the 4th frame at 43520ps is broken, but I somehow can't get rid of it. Can anybody help me? Best regards Hansjoerg Jerabek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
