[gmx-users] mdrun error

Justin Lemkul jalemkul at vt.edu
Sun Jul 21 13:14:30 CEST 2013

On 7/21/13 12:18 AM, Collins Nganou wrote:
> Dear Users,
> when trying to run the following command:
> mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
> I have received the error below.
> Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
> Starting 2 threads
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005
> Fatal error:
> Domain decomposition does not support simple neighbor searching, use grid
> searching or use particle decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I am looking any suggestion that can help me to overcome this error.

Not all combinations of options are compatible, and mdrun already told you 
exactly what to do.  If you want to use DD, you can't use "nstype = simple," so 
you have to invoke mdrun -pd in this case or otherwise switch to "nstype = 
grid."  How you proceed depends on what you're trying to achieve with your .mdp 



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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