[gmx-users] Domain Decomposition Error

Parker de Waal Parker.deWaal09 at kzoo.edu
Fri May 31 21:56:48 CEST 2013

Hi Everyone,

I'm trying to run energy minimization on my system and I am encountering
the following error:

Getting Loaded...
Reading file em.tpr, VERSION 4.5.5 (single precision)
Starting 16 threads
Loaded with Money

Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file

Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 10 nodes that is compatible with the
given box and a minimum cell size of 9.07242 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I've tested my bash script on a local server with an i7 and I've been able
to run error free, however when running on xsede resources I continually
encounter this error.

For information here is my bash:
grompp -f minim.mdp -c protein_solv_ions.gro -p protein.top -o em.tpr
mdrun -v -deffnm em
if [ ! $? == 0 ]
        echo "ERROR - Energy minimization"
        exit 5

and Here is my minim.mdp

integrator         = steep
emtol              = 10
emstep         = 0.01
nsteps             = 200
energygrps      = System

nstlist            = 5
ns_type            = grid
rlist              = 1.0
coulombtype        = PME
rcoulomb           = 1.0
rvdw               = 1.0
pbc                    = xyz

Any input would help!


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