Re: [gmx-users] remd jobs failed
Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- 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] remd jobs failed
hello David: thanks for kind reply. The .tpr file was created by grompp in cluster and there is no problem for that. thank you very much Albert On 10/19/2012 08:52 AM, Davide Mercadante wrote: Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- 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] remd jobs failed
Hi Albert, Please accept my apologies, I must have misread your e-mail. Effectively everything seems to be right in the command line and I am not able to understand either why you get the error. Good luck. Cheers, Davide On 19/10/12 7:54 PM, Albert mailmd2...@gmail.com wrote: hello David: thanks for kind reply. The .tpr file was created by grompp in cluster and there is no problem for that. thank you very much Albert On 10/19/2012 08:52 AM, Davide Mercadante wrote: Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- 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 -- 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] remd jobs failed
On 10/19/12 2:37 AM, Albert wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) You should be executing mdrun instead of g_tune_pme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
