[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

[lloyd riggs]

you have to play with the ratio usually of domain decompositions Vs. Grid size, I had that error some time ago though, if you look at the generated .mdp from the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and play with it.  It dosent like odd numbers or non-whole decompositions which are based on the cpu's versus total size.

fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0

I might have remembered the answer wrong though, but someone will correct me if I am wrong I hope.

PS, are you from LA.  Just asking I used to know someone with the exact same name, but I also vaguely remember seeing your name here and asking that once before...

Stephan Watkins

> I am performing a free energy calculation based on Justin Lemkul's
> tutorial.
> My system is a protein in water and dodecane and I'm coupling the protein
> considering none to only vdw interactions for my lambda 0 and 1 states.
> However, I get this error when trying to minimize the system:
> 
> Fatal error:
> There is no domain decomposition for 6 nodes that is compatible with the
> given box and a minimum cell size of 7.55833 nm min1.0.mdp
> <http://gromacs.5086.n6.nabble.com/file/n5001648/min1.0.mdp>  
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> 
> I know I can fix easily this problem by using -nt 1 option. But I still
> want
> to use all available cores. I suspect the error is in the mdp file because
> if I use the following mdp file for the minimization it works. 
> 
> title               =  cpeptide
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  1000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> 
> Obviously this mdp file does not work for free energy calculations. I
> still
> want to use the attached one, but I don´t know what to change to make it
> work.
> 
> This is the link for my log and mdp file.
> mdp_and_log_files.zip
> <http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip>  
> 
> Thank you in advance, 
> 
> Sonia Aguilera
> Graduate Assistant
> Universidad de los Andes-Colombia
> 
> 
> 
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