thanks Mark! could you please also confirm that my method of the prolongation of the simulation would be correct
#entend simulation for 50 ns and save these pieces as the separate files with the name step7_2* gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 50000 mdrun -v -deffnm step7_2 -cpi step7_1.cpt 2018-06-22 10:57 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > The previous checkpoint has the _prev suffix, in case there is a problem > that might require you to go further back in time. > > Mark > > On Fri, Jun 22, 2018, 10:46 Own 12121325 <own12121...@gmail.com> wrote: > > > P.S. what the difference between name.cpt and name_prev.cpt produced by > > mdrun? What check-point should correspond to the last snapshot in trr > file > > ? > > > > 2018-06-22 10:17 GMT+02:00 Own 12121325 <own12121...@gmail.com>: > > > > > 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. > > > -- > 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.