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

[Mark Abraham]

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
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> >>>>
> >>>>
> >> --
> >> ==================================================
> >>
> >> 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!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> >>
> >
> >
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