Re: [gmx-users] trn file
Maurício Menegatti Rigo wrote: With gmxcheck, I have the following: *Checking file File1.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 47639 Last frame 12 time 14.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File2.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 15.000 # Atoms 47639 Last frame 12 time 19.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File3.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 20.000 # Atoms 47639 Last frame 12 time 24.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File4.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 25.000 # Atoms 47639 Last frame 12 time 29.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File5.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 30.000 # Atoms 47639 Reading frame 70 time 58.000 --- Program gmxcheck, VERSION 4.0.7 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- This means that my FIle5.trr stopped at time 58. (the correct would be 2000.)? IS THere any way to fix it? Thanks ! Not likely. If a frame is corrupt, tools like trjconv that can parse them out generally fail as well. You can, however, use trjconv -e 58 to save the first frames of "File5.trr" and then continue on from a checkpoint to re-collect the remaining data. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] trn file
With gmxcheck, I have the following: *Checking file File1.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 47639 Last frame 12 time 14.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File2.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 15.000 # Atoms 47639 Last frame 12 time 19.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File3.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 20.000 # Atoms 47639 Last frame 12 time 24.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File4.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 25.000 # Atoms 47639 Last frame 12 time 29.800 Item#frames Timestep (ps) Step130.4 Time130.4 Lambda 130.4 Coords 130.4 Velocities 130.4 Forces 0 Box 130.4 *Checking file File5.trr* trn version: GMX_trn_file (single precision) Reading frame 0 time 30.000 # Atoms 47639 Reading frame 70 time 58.000 --- Program gmxcheck, VERSION 4.0.7 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- This means that my FIle5.trr stopped at time 58. (the correct would be 2000.)? IS THere any way to fix it? Thanks ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] trn file
Maurício Menegatti Rigo wrote: HI, I'm extensivally searching at manual, internet, gmx-list but i cant find the solution for this error. I tried to concatenate several .trr files with the following line: trjcat -f File1.trr File2.trr File3.trr File4.trr File5.trr File6.trr File7.trr File8.trr -o FINAL File1 to File4 have no problems. HOwever, from File5 the program present the following error: /Continue writing frames from File5.trr t=30 ps, frame=76 Reading frame 70 time 58.000-> frame150 time 59.600 ps --- Program trjcat, VERSION 4.0.7 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- / What is this? Someone could help me on how to fix it? Or where I can find some literature to help me? What does gmxcheck tell you about the integrity of each of these files? Probably the file is corrupted (bad frame, etc). -Justin Thank you ! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] trn file
HI, I'm extensivally searching at manual, internet, gmx-list but i cant find the solution for this error. I tried to concatenate several .trr files with the following line: trjcat -f File1.trr File2.trr File3.trr File4.trr File5.trr File6.trr File7.trr File8.trr -o FINAL File1 to File4 have no problems. HOwever, from File5 the program present the following error: *Continue writing frames from File5.trr t=30 ps, frame=76 Reading frame 70 time 58.000-> frame150 time 59.600 ps --- Program trjcat, VERSION 4.0.7 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- * What is this? Someone could help me on how to fix it? Or where I can find some literature to help me? Thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
