[gmx-users] grompp for minimization: note & warning

Justin Lemkul jalemkul at vt.edu
Sun Sep 15 14:22:52 CEST 2013

On 9/15/13 8:17 AM, shahab shariati wrote:
> Dear gromacs users
> I used -maxwarn option, but after using this command:
> mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
> I encountered with:
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with the
> given box and a minimum cell size of 6.61528 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> Based on above suggestion, I should use option -rdd with mdrun, but I dont
> what argument with -rdd? What value is appropriate for -rdd? 0 or other?

Not all systems can be decomposed to run on any arbitrary number of cores/threads.


See my previous message for my thoughts on the error grompp gave you, as it 
relates to this one.  Regardless, running with -nt 1 will work and should 
complete reasonably quickly (EM shouldn't take too long).



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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