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

shahab shariati shahab.shariati at gmail.com
Sun Sep 15 14:17:58 CEST 2013

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?

Best wishes

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