Hello Justin, could you specify please a bit more. Following your method, if the simulation has been terminated by crash without producing gro file so to re-initiate it I only need one command:
gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append where the last_checkpoint should be something like initial.cpt or initial_prev.cpt but In case if my simulation has been finished correctly e.g. for 50 ns and I now need to extend it for another 50 ns, should I do the following trick with 2 GMX programs: gmx convert-tpr -s init.tpr -o next.tpr -extend 500000 gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append it will produce the second part of the trajectory as the new file (next.trr) or merge together the first and the second part ? Thank you! Gleb 2018-06-18 21:00 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 6/18/18 9:11 AM, Own 12121325 wrote: > >> thanks Justin for the suggestions! >> >> but generally this antiquated approach produces correct thermodynamical >> ensembles (since I do not call grompp again), doesn't it? Following this >> method the last snapshot from the trajectory will be taken to continue >> job, >> right ? >> > > Possibly. I haven't done this since the 3.3.x series, though, because > checkpoints guarantee an exact continuation. The combination of .trr + .edr > is not exact but is close. It probably all comes out in the noise of the > simulation, but if you can choose between an exact continuation and an > approximate one, why not be exact? :) > > -Justin > > > 2018-06-15 14:22 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> On 6/14/18 4:01 AM, Own 12121325 wrote: >>> >>> Hello, >>>> >>>> I wonder to know if it's necessary to provide edr file for the completed >>>> part of the simulation in order to continue the md job assuming that I >>>> provide the trajectory (with coordinates and velocities) using >>>> gmx convert-tpr. >>>> >>>> Does the ensembles produced by mdrun will be the same following these >>>> two >>>> methods of the continuation: >>>> >>>> gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 >>>> gmx mdrun -v -deffnm next >>>> >>>> compared to >>>> >>>> gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr >>>> -extend >>>> 1000 >>>> gmx mdrun -v -deffnm next >>>> >>>> You don't use either .trr or .edr files. Just generate the new .tpr file >>> with however much more time you want and pick up from the exact time >>> point >>> you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend >>> simulations is an antiquated approach. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> 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. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.