[gmx-users] error in mdrun

[Justin A. Lemkul]

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

-- 
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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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