[gmx-users] domain decomposition error

[Justin A. Lemkul]

Moeed wrote:
> Hello Justin,
> 
> I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and 
> even 3 number of processors. I read about domain decomposition on the 
> website and tried less number of processors, as just mentioned. My 
> understanting after reading about the error is that parallel simulation 
> is not working with a small system as mine! but there are 11000 atoms in 
> there and I am doing FE stuff... I dont see why this is considered as 
> small simulation!

This exact situation was just discussed last week regarding FEP and DD (hint: 
check the archive!).  If you set your intramolecular interactions to be computed 
as exclusions and pairs (i.e. couple_intramol=no), then you have (essentially) 
long-range bonded interactions.  Either use mdrun -pd or run in serial.

> =============================
> There is no domain decomposition for 4 nodes that is compatible with the 
> given box and a minimum cell size of 5.70044 nm
> Change the number of nodes or mdrun option -rdd or -dds
> =========================
> Also I checked the manual for  the options below but I have no clue what 
> value to set for my system.
> 
> 
> -rdd         real   0       The maximum distance for bonded interactions 
> with
>                             DD (nm), 0 is determine from initial coordinates
> 
> -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
> ***************************************
> 
> Thanks,
> Moeed
> 
> BTW: About mdp setting for electrostatics, I have set zero charges to 
> all atoms so there is no electrostatics term ( I have only C and H). 
> Thats why I commented out ;coulombtype         =  PME 
> 

For both solute and solvent?  Just one?  Seems like an unreasonable model to me. 
  Even hydrocarbons should have some (obviously offsetting) partial charge.

-Justin

> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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