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

[Yong Wang]

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
> > > --
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-- 

==========================
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