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

[Dr. Vitaly Chaban]

On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>


I can send you a couple of systems, which spontaneously crash. Not at the
beginning and not at the end, just unpredictably every few dozens of
nanoseconds. The systems are not strictly in the thermodynamic equilibrium
state, but they are not exploding in the common sense of this term. Another
coordinate files, executed with the same MDP file, never crash, however. I
do not really know the reason, but it is not as simple as good or bad set
of MD parameters. Maybe, something is connected with (deprecated) versions
of external libraries, since at my workstation, where I control everything,
crashes occur more rarely than at the cluster.




>
>  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?
>
>


Really? How many force fields can you enumerate, where the developers say
how we should distribute atoms among the charge groups?

Not all MD codes use charge group mechanism, by the way.

Anyways, this is not my thread. Perhaps, the starter really has a simple
problem with blowing up.


Dr. Vitaly Chaban












> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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