[gmx-users] Continuation of the gromacs job using gmx convert-tpr
Own 12121325
own12121325 at gmail.com
Fri Jun 22 16:22:56 CEST 2018
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+
> trajectory+&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
> > > > >>>>
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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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