[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation

[Tomek Wlodarski]

Dear Mark,

Thank you for suggestion.
I run plain mdrun to advance each simulation to the same time point and use
new cpt to restart replica exchange simulations.
It started without any error from the proper time point and metadynamics
was running OK.
However, when it finished it did not write any new cpt files... so when I
restarted it again it started from the the same time point like the one
before....
Any idea what may cause this problem?
Thank you.
Best,

tomek

On Tue, Oct 13, 2015 at 11:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Unfortunately, that should
> a) never happen,
> b) given a), rarely happen identically for successive checkpoints,
> c) is even more strange if your time step is a normal ~2fs, and
> d) is not easy to fix.
>
> To address a-c), it would be good for you to get some feedback from the
> PLUMED developers about whether others have reported such problems.
> Offhand, I don't know of any plain GROMACS user who's been able to produce
> such checkpoint files. Last time I looked at their code I didn't see
> anything that could do this, but that was 1.x. It is also conceivable that
> this is a bug in your MPI layer.
>
> For d), you can try
> * back up your files
> * use plain mdrun to advance all of the 194440.010 files by one step (e.g.
> gmx mdrun -nsteps 1 -s old -cpi state)
> * same for the 194440.002 files by as many steps as you need to catch up to
> the others
> * restart mdrun -multi -replex
>
> Simulations have an internal part number that is expected to match, which
> is why you can't just run an extra part to catch up the simulations that
> are lagging.
>
> Mark
>
> On Tue, Oct 13, 2015 at 12:05 PM Tomek Wlodarski <
> tomek.wlodarski at gmail.com>
> wrote:
>
> > Dear GROMACS users,
> >
> > I am running REMD simulation with Gromacs 5.0.4 and PLUMED 2.1 for
> already
> > around 200ns with many smooth restarts. Unfortunately now something went
> > wrong because I got error that:
> >
> > The 6 subsystems are not compatible
> >
> > So I checked with gmxcheck cpt files
> > replica 1: Last frame         -1 time 194440.010
> > replica 2: Last frame         -1 time 194440.010
> > replica 3: Last frame         -1 time 194440.010
> > replica 4: Last frame         -1 time *194440.002*
> > replica 5: Last frame         -1 time 194440.010
> > replica 6: Last frame         -1 time *194440.002*
> > Same situation is in _prev.cpt
> > replica 1: Last frame         -1 time 194400.010
> > replica 2: Last frame         -1 time 194400.010
> > replica 3: Last frame         -1 time 194400.010
> > replica 4: Last frame         -1 time *194400.002*
> > replica 5: Last frame         -1 time 194400.010
> > replica 6: Last frame         -1 time *194400.002*
> >
> > Any idea how to restart simulation when both cpt and _prev.cpt file seem
> to
> > be broken?
> > Why this happened and how to prevent it?
> > Thank you.
> > All the best,
> >
> > tomek
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