[gmx-users] Using the checkpoint file to restore corrupt trajectory.
Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-the-checkpoint-file-to-restore-corrupt-trajectory-tp5009851.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- 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] Using the checkpoint file to restore corrupt trajectory.
Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Using the checkpoint file to restore corrupt trajectory.
I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:52 AM, rajat desikan wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. You need a checkpoint file that corresponds to a good frame before the corruption. If you don't have that, you can't fix the broken trajectory. Your first message implied that you had a good frame. Since that's not the case, you'll have to either re-run the simulation or skip the bad frame and settle for fewer data points. -Justin On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- 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] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every -cpt minutes. You can keep all checkpoints by using the mdrun -cpnum option, but I suspect that will use up a lot of disk space. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. Or just re-run the simulation from the same .tpr file you used before. -Justin On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- 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] Using the checkpoint file to restore corrupt trajectory.
Thank you! On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every -cpt minutes. You can keep all checkpoints by using the mdrun -cpnum option, but I suspect that will use up a lot of disk space. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. Or just re-run the simulation from the same .tpr file you used before. -Justin On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
