[gmx-users] trjcat error of different spacing
Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 ps WARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjcat error of different spacing
Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 ps WARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjcat error of different spacing
Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjcat error of different spacing
Anirban Ghosh wrote: Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? I don't know yet. A few more questions: 1. What version of Gromacs are you using? 2. How many total trajectories are you concatenating? You said there was a problem from 10 - 300 ns, but I don't see any times shown here below 2957280. The real problem could be early on in the trajectory. -Justin Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjcat error of different spacing
Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Thanks, Anirban On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? I don't know yet. A few more questions: 1. What version of Gromacs are you using? 2. How many total trajectories are you concatenating? You said there was a problem from 10 - 300 ns, but I don't see any times shown here below 2957280. The real problem could be early on in the trajectory. -Justin Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] trjcat error of different spacing
Anirban Ghosh wrote: Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Run gmxcheck on all your trajectories. It is possible that something (very) early on is not matching with something much later. The flat line you reported in the g_sas output indicates that the problem may not be at 300 ns, but rather around 10 ns. What that problem is exactly is hard to say at this point, but you may have a corrupted frame somewhere in that interval that's throwing things off. -Justin Thanks, Anirban On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? I don't know yet. A few more questions: 1. What version of Gromacs are you using? 2. How many total trajectories are you concatenating? You said there was a problem from 10 - 300 ns, but I don't see any times shown here below 2957280. The real problem could be early on in the trajectory. -Justin Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] trjcat error
Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Any suggestion is welcome. Regards, Anirban On Fri, Dec 18, 2009 at 12:49 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 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] trjcat error
Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- 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] trjcat error
Thanks Mark for the reply. The simulation ran fine and at the end of the .log file I got the following line: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 125029.000 125029.000100.0 1d10h43:49 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:932.867 46.259 3.729 6.436 Finished mdrun on node 0 Fri Dec 11 22:58:06 2009 -- There was no error and I did not ran out of disk space. What should I do now? Can I repair this .trr file anyway? Any suggestion is welcome. Regards, Anirban On Fri, Dec 18, 2009 at 2:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- 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 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] trjcat error
Anirban Ghosh wrote: Thanks Mark for the reply. The simulation ran fine and at the end of the .log file I got the following line: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 125029.000 125029.000100.0 1d10h43:49 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:932.867 46.259 3.729 6.436 Finished mdrun on node 0 Fri Dec 11 22:58:06 2009 -- There was no error and I did not ran out of disk space. What should I do now? Can I repair this .trr file anyway? Any suggestion is welcome. Well if you haven't broken the file since (check its size), it was not written properly during the calculation. This sort of thing can happen with remote-mounted disks, etc. if the underlying filesystem is not solid. Mark On Fri, Dec 18, 2009 at 2:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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://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] trjcat error
Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- 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] trjcat error
Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] trjcat error
Dear all , I did a simulation for 2 ns then i extanded the simulation using tpbconv for another 2 ns. After that, I tried to combine the two trajectory files by using trjcat by using the following command: trjcat -f md1.xtc extend1.xtc -o combine.xtc but it showed a warning that it couldn't read the frame from file. This is the 1st time i use trjcat, so i am wonder whether the command is correct or have some problems with the files. QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjcat error
Hi QIU YI HUAN, Was it a warning or did it exit without producing output? Please be more complete in your postings. Maybe a good idea to include the output of the program? In case of an error use gmxcheck first on each of the trajectories. It seems that one of them is giving an error. Then, if you know which trajectory is wrong, you can use trjconv to read up to the bad frame, and write a good trajectory. Obviously, you'll miss what comes after the bad frame. Cheers, Tsjerk On 11/25/08, Q. Y. HUAN [EMAIL PROTECTED] wrote: Dear all , I did a simulation for 2 ns then i extanded the simulation using tpbconv for another 2 ns. After that, I tried to combine the two trajectory files by using trjcat by using the following command: trjcat -f md1.xtc extend1.xtc -o combine.xtc but it showed a warning that it couldn't read the frame from file. This is the 1st time i use trjcat, so i am wonder whether the command is correct or have some problems with the files. QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
