MIX = integer constant
MJX = integer constant
MKX = integer constant
MIX and MJX specify the horizontal grid dimensions of the largest domain that will be simulated by the model after it is compiled. MIX is the north-south grid dimension; MJX is the east west grid dimension. It is always possible to run smaller domains, but never larger. Always specify the total grid size of the largest domain, irrespective of what you may know about how many processors the code will run on. Reducing the size of the memory on each processor is handled by a separate mechanism.
MKX is the number of vertical levels (at half-sigma) for the scenario and it must be specified exactly for the scenario and an MM5 executable compiled to run, say, 25 levels cannot be used to run a 23 layer scenario without recompiling. There is no need to specify the number of full-sigma layers (which works out to MKX+1). The model takes care of this.