[gmx-users] A charge group moved too far between two domain decomposition steps

Justin Lemkul jalemkul at vt.edu
Tue Jun 11 15:52:01 CEST 2013

On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
> This problem indeed happens from time to time. With versions 4.5+ it is
> more frequent than with versions up to 4.0.7. It is not always connected to
> blowing up in the sense of bad contacts, positive potential energy, etc.
> The more cores you use per job, the more likely this error to appear. The
> larger *spatially) system you simulate, the more likely it to appear.

People generally reported more crashes in 4.5.x than in 4.0.x that we determined 
arise from nsttcouple and nstpcouple being set incorrectly.  There's a thread 
somewhere about it, but in general, the same principles are always true - 
adequate equilibration and sensible .mdp settings should lead to stable 
integration later on.

> The simple advice is to reduce the time-step, but it is not to be
> understood as a universal treatment.
> Of course, you can reinitialize your charge groups, as this is better
> connected with the below error message.

What does this mean?  Charge groups are a fixed element of the force field; how 
would you propose adjusting them to make the error go away?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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