[gmx-users] Fwd: Parallellization problem

[Nuria Alegret]

  Good afternoon,

I'm using GROMACS version 4.0.5. My simulation system is a double 
stranded DNA (51 nucleotides) in a water (TIPI3P type) box, defined as 
0.9 A from the DNA, with 100 Na ions to neutralize the system. The 
sequencial commands used were:

1) pdb2gmx -f dsDNA.pdb -p dsDNA.top -o dsDNA.gro -ffamber99

2) editconf -f dsDNA.gro -o box.gro -d 0.9

3) genbox -cp box.gro -cs ffamber_tip3p.gro -o water.gro -p dsDNA.top

4) grompp -f em.mdp -c water.gro -p dsDNA.top -o Premin.tpr

5) genion -s Premin.tpr -o water-ions.gro -np 100

6) grompp -f em.mdp -c water-ions.gro -p dsDNA.top -o minIons.tpr

7) MINIMIZATION:  mdrun -v -s minIons.tpr -o minIons_traj.trr -x 
minIons_traj.xtc -c minIons_final.gro -e minIons_ener.edr


The problem appears when I try to minimize the system. When I try to 
parallellize the calculation, the calculation returns with an error 
message as follows:

/Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the 
given box and a minimum cell size of 38.1122 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition/

According to your web page, this error appears when a very small system 
is too small to run parallellized. But my system is extremelly big!! In 
previous calcs I could parallellize smaller systems, even with just 8 
nucleotides.
I attach you the error file and the log file, as well as the mdp.
I would be gratefull with any help. Thanks in advance,



Núria Alegret
University Rovira i Virgili - Tarragona (Spain)


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