[gmx-users] how to modify the code to generate more controllable checkpoints to restart?

[Mark Abraham]

Hi,

Vitaly's suggestion is incomplete, inasmuch as there are things like
thermodynamic coupling algorithms that need to preserve information across
restarts that are not x/v/f, so don't get written to the .trr file. In the
old days, those were written to the .edr file, and the combination of .edr
and .trr was enough for a binary-identical continuation. That's still
possible, but the .cpt is much more convenient for the purpose. Note that
you will generally not be able to reproduce the same trajectory, even
though the restart is binary identical. See
http://www.gromacs.org/Documentation/Terminology/Reproducibility. But
anyway you were wanting to change parameters, so grompp -p new.top -t
old.cpt is your friend.

Mark

On Tue, Jan 26, 2016 at 2:04 PM Yong Wang <wyongciac at gmail.com> wrote:

> Hi Mark, thank you very much. It is really a good way to do it without
> touching the code. Although as you said, it is not a perfect solution, but
> I think it is sufficient to do what I want.
>
> Also thank you Vitaly for your comment. But I am not quite clear about the
> difference between the .cpt file and the .trr file. So can I really get an
> exact restart simulation from .trr file too? (here "exact" I mean the
> restarting trajectory will be exactly the same as the original trajectory).
> If so, why do we need to write the .cpt file?
>
> 2016-01-26 13:14 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > There's no need to modify the code to do this. You can schedule your own
> > halt e.g. 10ns from the end by choosing nsteps, save that checkpoint
> file,
> > and then continue. That's slightly wasteful of computer time, doing extra
> > shut-down and start-up work, but you can have it working in five minutes
> > ;-)
> >
> > Mark
> >
> > On Tue, 26 Jan 2016 12:22 VITALY V. CHABAN <vvchaban at gmail.com> wrote:
> >
> > > I suppose the TRR file, which you can write down at given frequency,
> > > contains the same information with the same precision as it is written
> > down
> > > to the CPT file.
> > >
> > >
> > >
> > >
> > >
> > > On Tue, Jan 26, 2016 at 7:50 AM, Yong Wang <wyongciac at gmail.com>
> wrote:
> > >
> > > > Hi,
> > > >
> > > > I'd like to restart the MD simulation from some time points (e.g.
> 10ns
> > > > before the end) but with minorly adjusted parameters. But it seems
> the
> > > > current Gromacs code can't do this right now.
> > > >
> > > > I am trying to understand how the checkpoints in gromacs work. But I
> > only
> > > > found very limited document about it:
> > > > "The checkpoint file is by default written to disc every 15 minutes
> > (and
> > > > always at the very end of a simulation), and it contains the latest
> > > > full-precision velocities, forces, and energies that are required to
> > > > continue a simulation, or restart a crashed-simulation. "
> > > >
> > > > Is it possible that we can control the output of checkpoint files as
> > > > flexibly as other files (e.g. .xtc or .edr) by introducing some mdp
> > > > options? More concretely, like using nstcptout=1000000 to write the
> > > > checkpoint files every 2ns with a suffix of md.cpt_${step}. I guess I
> > > have
> > > > to do some coding, but don't know if there will be too much work.
> Could
> > > > anyone show some guidance on this? Thanks.
> > > >
> > > > Yong
> > > >
> > > > --
> > > >
> > > > ==========================
> > > > Yong Wang
> > > > PhD Student, Structural Biology and NMR Laboratory (SBiNLab)
> > > > Department of Biology, University of Copenhagen, Denmark
> > > > Ole Maaloes Vej 5, DK-2200 Copenhagen N
> > > > https://www.researchgate.net/profile/Yong_Wang15
> > > > --
> > > > 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-request at 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-request at 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-request at gromacs.org.
> >
>
>
>
> --
>
> ==========================
> Yong Wang
> PhD Student, Structural Biology and NMR Laboratory (SBiNLab)
> Department of Biology, University of Copenhagen, Denmark
> Ole Maaloes Vej 5, DK-2200 Copenhagen N
> https://www.researchgate.net/profile/Yong_Wang15
> --
> 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-request at gromacs.org.
>