[gmx-users] restarting a replica exchange simulations

[Berk Hess]

> Date: Sat, 31 Jan 2009 01:30:11 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] restarting a replica exchange simulations
> 
> sarbani chattopadhyay wrote:
> >   Hi,
> >     I had previously ran a replica exchange molecular dynamics 
> > simulation for 10ns. There
> > were 17 ".tpr" input files for 17 replicas at 17 different temperatures.
> >             However, the run had stopped and now I need to restart it. I 
> > had generated 17 ".tpr"
> > files for the rest of the simulation left, using the  command "tpbconv", 
> > that is usually used for
> > generating ".tpr" file to restart a "md" run.
> >             Then again I gave the command for "mdrun" using "replex" 
> > option such that the input
> > files are the 17 new restart ".tpr " files.
> > 
> > Is this the right way to restart the replica exchange molecular dynamics 
> > simulation? Will the
> > trajectories of the 17 replicas start from the point inteneed and 
> > perform replica exchange as
> > per the command?
> 
> Under 3.x you need to apply a suitable, consistent tpbconv to each 
> independent simulation - see 
> http://wiki.gromacs.org/index.php/Doing_Restarts. Under 4.x the restart 
> mechanism has changed, and the checkpoint file is now the main thing you 
> have to take care of. I'll update the wiki once I've needed to work out 
> how that works.
> 
> Mark

Restarting from checkpoints is trivial for normal simulations.
But for REMD simulations there is currently no mechanism that ensures
that all replicas write checkpoints at the same step.
In 4.0.4 the replace setup will at least allow the checkpoint to
be at different steps at long at they are between the same exchange steps.
A proper solution will be implemented in 4.1.

But it seems that under normal conditions checkpoints will usually be written
at the same step for all replicas.

Berk


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