[gmx-users] replica restart from checkpoints

Berk Hess gmx3 at hotmail.com
Thu Feb 19 21:24:50 CET 2009


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.
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.
(you can always go back to using tpbconv)

Synchronizing the checkpoint writing is a bit complicated
and will probably only be done in 4.1.


> 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 run  
> 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 expressed
> 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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