[gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

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.abraham at 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 <own12121325 at 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 <own12121325 at 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 <jalemkul at 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 <jalemkul at 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
> > >>>>
> > >>>> jalemkul at 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!
> > >>>>
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> or
> > >>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>
> > >>>>
> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Assistant Professor
> > >> Virginia Tech Department of Biochemistry
> > >>
> > >> 303 Engel Hall
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at 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!
> > >>
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> > >>
> > >
> > >
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