[gmx-users] error in mdrun

[reisingere at rostlab.informatik.tu-muenchen.de]

I already decrease it to 0.002 as you said and then there comes this error
I wrote to you.
Now It try it with 0.001. It is still running.

Thank you for your answer.
Eva

>
>
> On 7/9/12 9:46 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> With the mentioned below options I get the following error:
>>
>> Fatal error:
>> 1 particles communicated to PME node 1 are more than 2/3 times the
>> cut-off
>> out of the domain decomposition cell of their charge group in dimension
>> x.
>> This usually means that your system is not well equilibrated.
>>
>>
>> But it does not occur immediatly but only at step
>>
>> Step 695, time 1.39 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 2.011725, max 78.611298 (between atoms 3778 and 3781)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>     3782   3785   92.2    1.3061   0.2785      0.1090
>>     3782   3784   93.0    0.1055   0.2552      0.1090
>>     3782   3783   91.0    0.1062   0.3086      0.1090
>>     3204   3206   89.6    0.1449   1.0256      0.1449
>>     3204   3205   89.7    0.1010   0.9949      0.1010
>>
>>
>> Is there something wrong with my temperature coupling?
>>
>
> I doubt it.  Decrease your timestep (as I've said twice now) and try again
> with
> something sensible for dt.
>
> -Justin
>
> --
> ========================================
>
> 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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>
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