Re: [gmx-users] restarting the crashed run
Thank you Justin for your reply. Pt 3 should be the correct way to proceed. But somehow if I have lost my state.cpt file, can I continue my run using following commands: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene -noappend trjcat -f previous.trr next.trr -o combine.trr On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coordinates, you're going to be dealing with the initial state, not the last state of the previous simulation, so that's garbage. If you're restarting a crash, then presumably there is no need at all to invoke tpbconv or grompp. and finally running mdrun but with no cpi option Makes no sense. You're basically obliterating the previous simulation. 2) same as 1 but with -cpi option Still no need for grompp, but if providing -cpi to mdrun, you're resuming from the correct state. 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) This is the correct way to proceed. The run will pick up from the state stored in the .cpt file and proceed with the number of steps originally specified in the .tpr file. 4) using procedure 3 but with no state.cpt file The run should start over. Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 Without a .cpt file, the run starts over from the beginning. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 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 -- 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] restarting the crashed run
No, because then the state.cpt file would be redundant :-) All you can do re-start from the beginning, because the .tpr file only has the initial state. You can extend the number of steps, but you can't magically produce the state after the first simulation just from the initial one. (If you can, you'll be hugely popular here, though!) Mark On Sun, Sep 22, 2013 at 12:03 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Thank you Justin for your reply. Pt 3 should be the correct way to proceed. But somehow if I have lost my state.cpt file, can I continue my run using following commands: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene -noappend trjcat -f previous.trr next.trr -o combine.trr On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coordinates, you're going to be dealing with the initial state, not the last state of the previous simulation, so that's garbage. If you're restarting a crash, then presumably there is no need at all to invoke tpbconv or grompp. and finally running mdrun but with no cpi option Makes no sense. You're basically obliterating the previous simulation. 2) same as 1 but with -cpi option Still no need for grompp, but if providing -cpi to mdrun, you're resuming from the correct state. 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) This is the correct way to proceed. The run will pick up from the state stored in the .cpt file and proceed with the number of steps originally specified in the .tpr file. 4) using procedure 3 but with no state.cpt file The run should start over. Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 Without a .cpt file, the run starts over from the beginning. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 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 -- 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] restarting the crashed run
Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file and finally running mdrun but with no cpi option 2) same as 1 but with -cpi option 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) 4) using procedure 3 but with no state.cpt file Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 -- 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] restarting the crashed run
On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coordinates, you're going to be dealing with the initial state, not the last state of the previous simulation, so that's garbage. If you're restarting a crash, then presumably there is no need at all to invoke tpbconv or grompp. and finally running mdrun but with no cpi option Makes no sense. You're basically obliterating the previous simulation. 2) same as 1 but with -cpi option Still no need for grompp, but if providing -cpi to mdrun, you're resuming from the correct state. 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) This is the correct way to proceed. The run will pick up from the state stored in the .cpt file and proceed with the number of steps originally specified in the .tpr file. 4) using procedure 3 but with no state.cpt file The run should start over. Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 Without a .cpt file, the run starts over from the beginning. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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
