[gmx-users] No domain decomposition

soumadwip ghosh soumadwipghosh at gmail.com
Thu Sep 24 12:28:24 CEST 2015

Please ignore the previous mail.

Hi all,
       I am simulating a swCNT-ssDNA hybrid ( dna encapsulated in CNT) in
the presence of some organic fillers. I made the topologies using pdb2gmx
and until the energy minimization mdrun step everything was fine. I used
the following command to for energy minimization

mdrun -deffnm em and I was stuck with the following error

There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 3.60353 nm
Change the number of nodes or mdrun option -rdd

Although I have seen a lot of discussions on this topic in the forum I did
not get the probable solution. I am using GROMACS 4.5.6 and the water model
employed is SPCE. Is there a possibility that my system topology is bad and
that is getting reflected here or by changing the no. of nodes or the -rdd
option the error can be tackled?

I am attaching my minim.mdp file here followed by the em.log file created.


; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 1000.0        ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep          = 0.001          ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor list and
long range forces
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short
range forces)
coulombtype     = PME           ; Treatment of long range electrostatic
rcoulomb        = 1.0           ; Short-range electrostatic cut-off
rvdw            = 1.0           ; Short-range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

and the em.log file (last few lines) as follows-

Initializing Domain Decomposition on 80 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 3.276 nm, LJ-14, atoms 1550 1554
  multi-body bonded interactions: 3.276 nm, Proper Dih., atoms 1550 1554
Minimum cell size due to bonded interactions: 3.604 nm
Guess for relative PME load: 0.31
Will use 56 particle-particle and 24 PME only nodes
This is a guess, check the performance at the end of the log file
Using 24 separate PME nodes, as guessed by mdrun
Optimizing the DD grid for 56 cells with a minimum initial size of 3.604 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2

I would appreciate any kind of help. In these cases do switching to a
higher version of GROMACS or take the help of MPI be helpful? I am sorry if
I am saying something stupid. I tried playing around with options such as
-nt, -npme and all but this error is still popping up.
Thanks for your time in advance.

Soumadwip Ghosh
Research Fellow

More information about the gromacs.org_gmx-users mailing list