Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 5
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 5
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 5
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 :
> 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 5
> 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 5
> mdrun -v -deffnm step7_2
>
>
>
> 2018-06-22 15:02 GMT+02:00 Mark Abraham :
>
>> 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
>> 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 5
>> > mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>> >
>> > 2018-06-22 10:57 GMT+02:00 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
>> 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 :
>> > > >
>> > > > > 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 5
>> > > > > 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
>>
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 5
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 5
mdrun -v -deffnm step7_2
2018-06-22 15:02 GMT+02:00 Mark Abraham :
> 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
> 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 5
> > mdrun -v -deffnm step7_2 -cpi step7_1.cpt
> >
> > 2018-06-22 10:57 GMT+02:00 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
> 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 :
> > > >
> > > > > 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 5
> > > > > 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 :
> > > > >
> > > > >>
> > > > >>
> > > > >> 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 50
> > > > >>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
> > > > >>>
> > > > >>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
> > > > >>>
> > > > >>>
> > > > 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: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 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 5
> mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>
> 2018-06-22 10:57 GMT+02:00 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 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 :
> > >
> > > > 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 5
> > > > 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 :
> > > >
> > > >>
> > > >>
> > > >> 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 50
> > > >>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
> > > >>>
> > > >>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
> > > >>>
> > > >>>
> > > 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 50
> > > > 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
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 5
mdrun -v -deffnm step7_2 -cpi step7_1.cpt
2018-06-22 10:57 GMT+02:00 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 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 :
> >
> > > 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 5
> > > 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 :
> > >
> > >>
> > >>
> > >> 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 50
> > >>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
> > >>>
> > >>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
> > >>>
> > >>>
> > 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 50
> > > 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
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 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 :
>
> > 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 5
> > 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 :
> >
> >>
> >>
> >> 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 50
> >>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
> >>>
> >>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
> >>>
> >>>
> 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 50
> > 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
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> 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
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 :
> 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 5
> 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 :
>
>>
>>
>> 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 50
>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
>>>
>>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
>>>
>>>
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 50
> 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
==
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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!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 5
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 :
>
>
> 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 50
>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
>>
>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
>>
>>
>>> 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 50
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
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 50 gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt 2018-06-21 1:12 GMT+02:00 Justin Lemkul : 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 50 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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
and without append flag it will produce an output in the separate file, won't it? gmx convert-tpr -s init.tpr -o next.tpr -extend 50 gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt 2018-06-21 1:12 GMT+02:00 Justin Lemkul : > > > 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 50 >> 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. > -- 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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 50 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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
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 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 50 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 ? Thank you! Gleb 2018-06-18 21:00 GMT+02:00 Justin Lemkul : > > > On 6/18/18 9:11 AM, Own 12121325 wrote: > >> thanks Justin for the suggestions! >> >> but generally this antiquated approach produces correct thermodynamical >> ensembles (since I do not call grompp again), doesn't it? Following this >> method the last snapshot from the trajectory will be taken to continue >> job, >> right ? >> > > Possibly. I haven't done this since the 3.3.x series, though, because > checkpoints guarantee an exact continuation. The combination of .trr + .edr > is not exact but is close. It probably all comes out in the noise of the > simulation, but if you can choose between an exact continuation and an > approximate one, why not be exact? :) > > -Justin > > > 2018-06-15 14:22 GMT+02:00 Justin Lemkul : >> >> >>> On 6/14/18 4:01 AM, Own 12121325 wrote: >>> >>> Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles produced by mdrun will be the same following these two methods of the continuation: gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 gmx mdrun -v -deffnm next compared to gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend 1000 gmx mdrun -v -deffnm next You don't use either .trr or .edr files. Just generate the new .tpr file >>> with however much more time you want and pick up from the exact time >>> point >>> you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend >>> simulations is an antiquated approach. >>> >>> -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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
On 6/18/18 9:11 AM, Own 12121325 wrote: thanks Justin for the suggestions! but generally this antiquated approach produces correct thermodynamical ensembles (since I do not call grompp again), doesn't it? Following this method the last snapshot from the trajectory will be taken to continue job, right ? Possibly. I haven't done this since the 3.3.x series, though, because checkpoints guarantee an exact continuation. The combination of .trr + .edr is not exact but is close. It probably all comes out in the noise of the simulation, but if you can choose between an exact continuation and an approximate one, why not be exact? :) -Justin 2018-06-15 14:22 GMT+02:00 Justin Lemkul : On 6/14/18 4:01 AM, Own 12121325 wrote: Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles produced by mdrun will be the same following these two methods of the continuation: gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 gmx mdrun -v -deffnm next compared to gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend 1000 gmx mdrun -v -deffnm next You don't use either .trr or .edr files. Just generate the new .tpr file with however much more time you want and pick up from the exact time point you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend simulations is an antiquated approach. -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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
thanks Justin for the suggestions! but generally this antiquated approach produces correct thermodynamical ensembles (since I do not call grompp again), doesn't it? Following this method the last snapshot from the trajectory will be taken to continue job, right ? 2018-06-15 14:22 GMT+02:00 Justin Lemkul : > > > On 6/14/18 4:01 AM, Own 12121325 wrote: > >> Hello, >> >> I wonder to know if it's necessary to provide edr file for the completed >> part of the simulation in order to continue the md job assuming that I >> provide the trajectory (with coordinates and velocities) using >> gmx convert-tpr. >> >> Does the ensembles produced by mdrun will be the same following these two >> methods of the continuation: >> >> gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 >> gmx mdrun -v -deffnm next >> >> compared to >> >> gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend >> 1000 >> gmx mdrun -v -deffnm next >> > > You don't use either .trr or .edr files. Just generate the new .tpr file > with however much more time you want and pick up from the exact time point > you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend > simulations is an antiquated approach. > > -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. > -- 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.
Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr
On 6/14/18 4:01 AM, Own 12121325 wrote: Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles produced by mdrun will be the same following these two methods of the continuation: gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 gmx mdrun -v -deffnm next compared to gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend 1000 gmx mdrun -v -deffnm next You don't use either .trr or .edr files. Just generate the new .tpr file with however much more time you want and pick up from the exact time point you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend simulations is an antiquated approach. -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.
[gmx-users] Continuation of the gromacs job using gmx convert-tpr
Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles produced by mdrun will be the same following these two methods of the continuation: gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000 gmx mdrun -v -deffnm next compared to gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend 1000 gmx mdrun -v -deffnm next Thanks you in advance! -- 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.
