[gmx-users] Checkpoint files not being written

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 10 17:08:26 CEST 2010

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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