[gmx-users] replica restart from checkpoints
massimiliano.bonomi at gmail.com
Thu Feb 19 22:47:23 CET 2009
Thanks for your reply...
> Which version are you using?
> In 4.0.3 I made things slightly better by allowing checkpoints
> to have different step numbers, as long as they fall within
> the same exchange attempt steps.
I'm using 4.0.3. Same problem with the former versions 4.0.x.
> This could still cause problems when the steps in the checkpoints
> differ very much. But if you use -maxh all simulations should finish
> closely within each other.
Actually I'm using -maxh!
> (you can always go back to using tpbconv)
Unfortunately I have no trr files, but just xtc with only solute...
> Synchronizing the checkpoint writing is a bit complicated
> and will probably only be done in 4.1.
Is it not possible to define the writing stride in terms of MD steps?
> > From: massimiliano.bonomi at gmail.com
> > To: gmx-users at gromacs.org
> > Date: Thu, 19 Feb 2009 20:14:15 +0100
> > Subject: [gmx-users] replica restart from checkpoints
> > Dear Gromacs Users,
> > I'm experiencing some problems when restarting a replica exchange
> > from previous checkpoint files.
> > It often happens to me that the number of MD steps done in the
> > previous run is not the
> > same for all the replica. If this is the case, the program stops.
> > This may happen since checkpoints are written with a stride
> > in REAL time (every 15 minutes) and replica on different processors
> > may have run
> > for different number of steps in the same amount of time.
> > Is it possible to specify the checkpoint writing stride in number of
> > steps instead of real time?
> > Regards,
> > Massimiliano Bonomi
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