[gmx-users] question about continuation using tpbconv and mdrun -cpi

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 29 10:09:00 CEST 2009

Baofu Qiao wrote:
> Hi Mark,
> Thanks!
> Because the maximum time for one single job is set to be 24hours on the
> cluster I'm using, I want to make sure which is the best way to continue
> the gmx jobs. I wonder how strong effect "mdrun -cpi" has?  From the
> introduction of mdrun, it seems that there are some EXTRA energy frames,
> but for the trajectory file (.xtc), there is no extra frames? Am I right?
> "mdrun -h
> --> The contents will be binary identical (unless you use dynamic load
> balancing), but for technical reasons there might be some extra energy
> frames when using checkpointing (necessary for restarts without appending)."

The intent with GROMACS 4.x is for a user to be able to construct a .tpr 
with a very long simulation time, and perhaps constrain mdrun with -maxh 
(or rely on the cluster killing the job), and to use the information in 
the checkpoint file to restart correctly and perhaps to then use mdrun 
-append so that when the simulation is running smoothly, only one set of 
files needs to exist. Thus one doesn't need to trouble with using 
tpbconv correctly, crashes can restart transparently, etc. The old-style 
approach still works, however.

Obviously you should (be able to) verify with mdrun -reprod that 
whatever approach you use when you construct your job scripts leads to 
simulations that are in principle reproducible. For production, don't 
use -reprod because you will want the better speed from dynamic load 
balancing, etc.


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