[gmx-users] Checkpoint files not being written

Berk Hess gmx3 at hotmail.com
Fri Sep 10 17:58:33 CEST 2010


Do you have no cut-off's and nstlist set to 0?
That's the only case where I could see that checkpoints are missing.
If that's the case, please file a bugzilla so we don't forget to fix this for 4.5.2.

PS -cpnum has nothing to do with this.
I guess it's the bCPT = assignment in md.c that only gets set at NS steps or the last step.


> Date: Fri, 10 Sep 2010 11:08:26 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Checkpoint files not being written
> Hi All,
> I don't know if this is a new (intended) feature or a bug, so I figured I'd ask 
> :)  I'm running version 4.5.1 to do some implicit solvent simulations.  What 
> I've noticed is that, no matter how long the simulation runs, I only ever get a 
> checkpoint file at the end of the simulation, and thus the checkpoint interval 
> (which I have left at the default value of 15) is ignored.  All the simulations 
> I've done are sufficiently long (at least one hour) such that they should have 
> produced checkpoint files according to this interval.
> Could this issue be related to the introduction of the -cpnum flag, which is set 
> to "no" by default?  I've poked around a bit in the mdrun code, but I easily 
> lose my place trying to trace what's going on.  I've tried specifically adding 
> -cpnum to my mdrun command line, but still I am not receiving any intermediate 
> checkpoint files at the requested -cpt interval.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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