[gmx-users] Continuation of the gromacs job using gmx convert-tpr
Own 12121325
own12121325 at gmail.com
Sun Jun 24 13:06:29 CEST 2018
update:
I am trying using the way that you have suggested me
# the first step
gmx convert-tpr -s old.tpr -o new.tpr -extend 50000
mdrun_mpi -s new.tpr -deffnm old -cpi old -append
Here there is an issue:
Each time all pieces of the files will be merged into "old" (.trr .edr and
.cpt). But since I use always -deffnm old, the new check-point produced at
the end of the simulation will be always of the same name as the input
check-point (provided in the beginning)
so by the end of the each run I have to rename checkpoint file from old.cpt
to new.cpt and the next step should be
# the second step
gmx convert-tpr -s new.tpr -o new2.tpr -extend 50000
mdrun_mpi -s new2.tpr -deffnm old -cpi new -append
mv new.cpt new2.cpt
# the third step
gmx convert-tpr -s new2.tpr -o new3.tpr -extend 50000
mdrun_mpi -s new3.tpr -deffnm old -cpi new2 -append
mv new2.cpt new3.cpt
etc.
So the trajectory and edr files will be always the same but check-point
files updated (if I will be needed to go back )
Actually it may produce some mismatching between the files...
2018-06-22 16:22 GMT+02:00 Own 12121325 <own12121325 at gmail.com>:
> Thanks Mark!
>
>
> assuming that I am interesting to obtain separate files for the each step
> I need just one command:
>
> mdrun -v -deffnm step7_1 -cpi step7_1.cpt -noappend
> that each time should create step7_1part002 etc
>
> but in case if I want to set manes of each pieces manually (it sounds
> crazy but in fact I need to do follow this way!) does the method with gmx
> convert-tpr in principle produce separate pieces correctly?
>
> gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 50000
> mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>
> in earlier versions I did in the same way but without cpt file and it
> worked good:
>
> gmx convert-tpr -s step7_1.tpr -trr step7_1 -edr step7_1 -o step7_2.tpr
> -extend 50000
> mdrun -v -deffnm step7_2
>
>
>
> 2018-06-22 15:02 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
>> Hi,
>>
>> There are some differences in recent GROMACS versions here (because the
>> old
>> implementations were not robust enough), but the checkpoint restart will
>> not work with appending unless it finds the output files named in the .cpt
>> match those on the command line (here, from -deffnm). You're making extra
>> work for yourself in several ways.
>>
>> I encourage you to not use -deffnm with a new name that merely signifies
>> that the extension happened. There's no physical and no real
>> organizational
>> reason to do this.
>>
>> If you want numbered output files for each step, then start your
>> simulations with -noappend and let mdrun number them automatically. But
>> IMO
>> all that does is make work for you later, concatenating the files again.
>>
>> If you want appending to work after extending to the number of steps, use
>> -s new.tpr -deffnm old rather than -deffnm new, because the former doesn't
>> create name mismatches between those output files that the checkpoint
>> remembers and those you've instructed mdrun to use now.
>>
>> And if your reason for using -deffnm is that you want to have multiple
>> simulation steps in the same directory, bear in mind that using a single
>> directory to contain a single step is much more robust (you are using the
>> standard way of grouping related files, called a directory, and using cd
>> is
>> not any more difficult than -deffnm), and you can just use the default
>> file
>> naming:
>>
>> (cd step7; mpirun -np whatever gmx_mpi mdrun -s extended)
>>
>> Mark
>>
>> On Fri, Jun 22, 2018 at 11:07 AM Own 12121325 <own12121325 at gmail.com>
>> wrote:
>>
>> > 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
>> > <https://maps.google.com/?q=roduce+the+second+part+of+the+tr
>> ajectory+&entry=gmail&source=g>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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>> > > > >>>>
>> > > > >>>>
>> > > > >> --
>> > > > >> ==================================================
>> > > > >>
>> > > > >> 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
>> > > > >>
>> > > > >> ==================================================
>> > > > >>
>> > > > >> --
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