Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,After some googling, and tweaking with the mdp parameters (step size), I think I have managed to produce the ener.edr and ultimately the ener.xvg files.Anyway, the same problem occured at the same atom each time after an energy minimisation calculation, pointing at the same atom, irregardless of my "emstep".So, I went to my structure(.gro) file and made some changes to the problematic atom (atom 33772) by moving the atomic coordinates of 33772, 33773 and 33774 along the z-direction. I did that because the atom belongs to a water molecule.After that, the "ndx" and "tpr" files were updated.The subsequent energy minimisation based on the amended "gro" file fixed the issue, albeit with further corrections to other atoms/molecules.The confout.gro and ener.edr files were then produced alright.Kester- 원본 메일 -보낸사람 : Kester Wong kester2...@ibs.re.kr받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 11:57:30제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?Hi Justin,I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.The md.log file reports:Steepest Descents converged to machine precision in 14 steps,but did not reach the requested Fmax 200.Potential Energy = 7.9771407e+19Maximum force = inf on atom 33772Norm of force = infI guess this issue would be corrected using emtol = 1000?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 01:44:08제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?On 8/18/14, 8:15 AM, Kester Wong wrote: Hi Justin, THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine. Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation. For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files. Are sensible energies reported in the corresponding .log file? A run may "finish" but yield infinite energies if something failed. That can also lead to an incorrect interpretation of .edr contents. Again, running gmxcheck on all output files can be useful here. -Justin Regards, Kester - 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 8월 18일(월) 20:56:56 *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility
[gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Dear all,After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file.However, of all the energy minimised structures I have, one did not work.I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvgAs the same procedure worked for all my other structures, this fatal error read:Program g_energy_mpi, VERSION 5.0Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822Fatal error:Energy file ener.edr not recognized, maybe different CPU?The xvg file was successfully produced for other structures, why did it fail on this particular system?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file ener.edr to ener.xvg using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine.Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation.For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files.Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 18일(월) 20:56:56제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
On 8/18/14, 8:15 AM, Kester Wong wrote: Hi Justin, THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine. Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation. For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files. Are sensible energies reported in the corresponding .log file? A run may finish but yield infinite energies if something failed. That can also lead to an incorrect interpretation of .edr contents. Again, running gmxcheck on all output files can be useful here. -Justin Regards, Kester - 원본 메일 - *보낸사람* : Justin Lemkul jalem...@vt.edu *받는사람* : gmx-us...@gromacs.org *받은날짜* : 2014년 8월 18일(월) 20:56:56 *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file ener.edr to ener.xvg using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.The md.log file reports:Steepest Descents converged to machine precision in 14 steps,but did not reach the requested Fmax 200.Potential Energy = 7.9771407e+19Maximum force = inf on atom 33772Norm of force = infI guess this issue would be corrected using emtol = 1000?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 01:44:08제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 8:15 AM, Kester Wong wrote: Hi Justin, THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine. Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation. For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files. Are sensible energies reported in the corresponding .log file? A run may "finish" but yield infinite energies if something failed. That can also lead to an incorrect interpretation of .edr contents. Again, running gmxcheck on all output files can be useful here. -Justin Regards, Kester - 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 8월 18일(월) 20:56:56 *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.