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

[Sonia Aguilera]

Hi, 

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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