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

[Mark Abraham]

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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