In fact there is an alternative trick :-) If I rename a tpr file via gmx convert-tpr and then run mdrun using this new tpr as well as previous checkpoint, it will produce all pieces of the trajectory in the separate file:
gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 50000 mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt If I add -noappend flag to the mdrun, its also do the same job but also will add suffix pat002 to each of the new file (that is not necessary for me since I have already renamed tpr). Gleb 2018-06-21 14:17 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 6/21/18 2:35 AM, Own 12121325 wrote: > >> and without append flag it will produce an output in the separate file, >> won't it? >> > > No, because appending is the default behavior. Specifying -append just > invokes what mdrun does on its own. If you want a separate file, add > -noappend to your mdrun command. > > -Justin > > > gmx convert-tpr -s init.tpr -o next.tpr -extend 500000 >> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt >> >> 2018-06-21 1:12 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> On 6/19/18 4:45 AM, Own 12121325 wrote: >>> >>> 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 >>>> >>>> Right. >>> >>> 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 ? >>>> >>>> You're specifying -append, so the output will be concatenated by mdrun. >>> That's also been default behavior for as long as I can remember, too :) >>> >>> -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.