Re: [gmx-users] Restarting a crashed MD run
[EMAIL PROTECTED] wrote: sorry to ask again, I hope this is my last question about this. since I know now that the restarted run I did started from 0 time. I killed the job and it wrote velocity for the last frame. So since i knew i have to contiune this run that I just killed, I used tpbconj and it wrote a new tpr file and it said it will restart it from the time I killed the job ( half the simulation). SO i think I am set now to continue the simulation this way. The first time you used it, it will also have told you the frame it was going to be able to start from. The output messages are usually very thorough and helpful. Read them carefully and think about what they mean! :-) Thank you. I will save some energies and velocities in future simulations. but in this email, my job was not crashed..I terminated it and it wrote the last velocities and when i wanted to contiune it using pbdconj, it said it will finish the simulation from the time I terminated it. so is this accurate enough to finish it? Maybe. To get an exact continuation of some runs with temperature and/or pressure coupling you need to supply an .edr file. If you don't give one and it wanted one, tpbconv will warn you. Had you read the man page to tpbconv closely before using it, you would have been aware of these issues already. It describes why you had all of the problems that you had. You would have saved yourself and the mailing list some time :-) Please make a habit of searching manuals, man pages and mailing list archives before asking. Mark ___ 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] Restarting a crashed MD run
Thank you. I will save some energies and velocities in future simulations. but in this email, my job was not crashed..I terminated it and it wrote the last velocities and when i wanted to contiune it using pbdconj, it said it will finish the simulation from the time I terminated it. so is this accurate enough to finish it? thank u > Is it not better to save energies also once in a while along with the > velocities to make sure the restart of a crashed simulation is > correct. > > On 5/1/07, David van der Spoel <[EMAIL PROTECTED]> wrote: >> [EMAIL PROTECTED] wrote: >> > sorry to ask again, I hope this is my last question about this. >> > >> > since I know now that the restarted run I did started from 0 time. I >> > killed the job and it wrote velocity for the last frame. So since i >> knew i >> > have to contiune this run that I just killed, I used tpbconj and it >> wrote >> > a new tpr file and it said it will restart it from the time I killed >> the >> > job ( half the simulation). SO i think I am set now to continue the >> > simulation this way. >> > >> > Thank u >> > >> > >> > >> If your simulation crashes without saving to the trr you'll have to >> restart from your last tpr again. >> >> It would be more systematic to save velocities every once in a while, >> depending on how much time you can afford to lose. >> >> >> -- >> David. >> >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: 46 18 471 4205 fax: 46 18 511 755 >> [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se >> >> ___ >> 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 >> > > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. > ___ > 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 > > > ___ 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] Restarting a crashed MD run
Is it not better to save energies also once in a while along with the velocities to make sure the restart of a crashed simulation is correct. On 5/1/07, David van der Spoel <[EMAIL PROTECTED]> wrote: [EMAIL PROTECTED] wrote: > sorry to ask again, I hope this is my last question about this. > > since I know now that the restarted run I did started from 0 time. I > killed the job and it wrote velocity for the last frame. So since i knew i > have to contiune this run that I just killed, I used tpbconj and it wrote > a new tpr file and it said it will restart it from the time I killed the > job ( half the simulation). SO i think I am set now to continue the > simulation this way. > > Thank u > > > If your simulation crashes without saving to the trr you'll have to restart from your last tpr again. It would be more systematic to save velocities every once in a while, depending on how much time you can afford to lose. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ 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] Restarting a crashed MD run
[EMAIL PROTECTED] wrote: sorry to ask again, I hope this is my last question about this. since I know now that the restarted run I did started from 0 time. I killed the job and it wrote velocity for the last frame. So since i knew i have to contiune this run that I just killed, I used tpbconj and it wrote a new tpr file and it said it will restart it from the time I killed the job ( half the simulation). SO i think I am set now to continue the simulation this way. Thank u If your simulation crashes without saving to the trr you'll have to restart from your last tpr again. It would be more systematic to save velocities every once in a while, depending on how much time you can afford to lose. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Restarting a crashed MD run
sorry to ask again, I hope this is my last question about this. since I know now that the restarted run I did started from 0 time. I killed the job and it wrote velocity for the last frame. So since i knew i have to contiune this run that I just killed, I used tpbconj and it wrote a new tpr file and it said it will restart it from the time I killed the job ( half the simulation). SO i think I am set now to continue the simulation this way. Thank u > [EMAIL PROTECTED] wrote: >> Hi, >> >> I ran gmxcheck and 0 frames have velocities. >> >> so it means it started from beginning? >> >> Belquis >> >> > yes. > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ___ > 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 > > > ___ 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] Restarting a crashed MD run
[EMAIL PROTECTED] wrote: Hi, I ran gmxcheck and 0 frames have velocities. so it means it started from beginning? Belquis yes. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Restarting a crashed MD run
Hi, I ran gmxcheck and 0 frames have velocities. so it means it started from beginning? Belquis > [EMAIL PROTECTED] wrote: >> Hi Tsjerk, >> >> thank u for the answer. I checked my mdp file (nstvout=0). I just want >> to >> make sure that since nstvout=0 in my mdp file, and I used tpbconv >> means >> that it generated the run from the beginning of the crashed run? not >> the >> last frame? i >> >> > run gmxcheck on your trr file to see how many frames you have with > velocities. > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ___ > 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 > > > ___ 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] Restarting a crashed MD run
[EMAIL PROTECTED] wrote: Hi Tsjerk, thank u for the answer. I checked my mdp file (nstvout=0). I just want to make sure that since nstvout=0 in my mdp file, and I used tpbconv means that it generated the run from the beginning of the crashed run? not the last frame? i run gmxcheck on your trr file to see how many frames you have with velocities. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Restarting a crashed MD run
Hi Tsjerk, thank u for the answer. I checked my mdp file (nstvout=0). I just want to make sure that since nstvout=0 in my mdp file, and I used tpbconv means that it generated the run from the beginning of the crashed run? not the last frame? i Belquis > Hi Belquis, > > I think you have the same problem mentioned on this list a short while > ago: you're trajectory (.trr) probably didn't contain velocities other > than the first frame. Check the .mdp options (nstvout). > > Cheers, > > Tsjerk > > On 5/1/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >> Hello all, >> >> I restarted a crashed run due to power outage using these command >> lines: >> >> tpbconv -s md0-30ns.tpr -f md0-30ns.trr -e md0-30ns.edr -o >> md0-30ns-C.tpr >> >> then >> >> >> mdrun -s md0-30ns-C.tpr -e md0-30ns-C.edr -o md0-30ns-C.trr -x >> md0-30ns-C.xtc -c after_md0-30ns-C.gro -g md0-30ns-C.log >> >> >> The run was for 30 ns..However the new tpr started from time zero and >> it >> didnt do a continuation run from the crashed md. it is doing the whole >> 30 >> ns again, instead of completing what was left from the first run. It >> seems >> I am missing something? would anyone plz direct me on how to do this? >> >> Thank you >> >> Belquis >> >> ___ >> 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 > > > ___ 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] Restarting a crashed MD run
Hi Belquis, I think you have the same problem mentioned on this list a short while ago: you're trajectory (.trr) probably didn't contain velocities other than the first frame. Check the .mdp options (nstvout). Cheers, Tsjerk On 5/1/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Hello all, I restarted a crashed run due to power outage using these command lines: tpbconv -s md0-30ns.tpr -f md0-30ns.trr -e md0-30ns.edr -o md0-30ns-C.tpr then mdrun -s md0-30ns-C.tpr -e md0-30ns-C.edr -o md0-30ns-C.trr -x md0-30ns-C.xtc -c after_md0-30ns-C.gro -g md0-30ns-C.log The run was for 30 ns..However the new tpr started from time zero and it didnt do a continuation run from the crashed md. it is doing the whole 30 ns again, instead of completing what was left from the first run. It seems I am missing something? would anyone plz direct me on how to do this? Thank you Belquis ___ 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
