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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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