From SIMION
How do I change the grid scaling in a PA file to something other than 1 mm per grid unit?
A PA file in itself doesn't have physical units. A PA file is simply unit-less 2D or 3D matrix of grid points.
The physical size of your PA instances is instead determined by the workbench (IOB) file that references the PA instances. The size is controlled by the scale factor specified via the blue "mm/gu" (mm per grid unit) field in the Edit function under the PAs tab in the Ion Optics Workbench. The default is 1 mm/gu. In fact, you can assign a different scaling to each PA instance in your workbench, and multiple instances of the *same* PA file can be assigned different scaling factors as well.
Typically, one first selects any grid size that is appropriate in terms of computational quality and memory/time requirements. Then, one sets the scaling factor in the IOB file so that the PA is of the correct physical dimensions.
If using geometry files, see the "\Advanced SIMION Class\Reference\Geometry Files\a. Suggestions" section of the Advanced SIMION course (included on the SIMION 7.0 CD). In particular, to make things easier, it is typically recommended that you specify an appropriate scale in the "locate" command such that dimensions in your GEM file correspond exactly to physical dimensions.
; note: gu = "grid unit"
Pa_define(11,11,11,p,xyz) ; 0.025 in/gu or 0.635 mm/gu
;Pa_define(26,26,26,p,xyz) ; 0.010 in/gu or 0.254 mm/gu
;Pa_define(51,51,51,p,xyz) ; 0.005 in/gu or 0.127 mm/gu
;Pa_define(101,101,101,p,xyz) ; 0.0025 in/gu or 0.0635 mm/gu
Locate(0,0,0,40) ; 0.025 in/gu or 0.635 mm/gu
;Locate(0,0,0,100) ; 0.010 in/gu or 0.254 mm/gu
;Locate(0,0,0,200) ; 0.005 in/gu or 0.127 mm/gu
;Locate(0,0,0,400) ; 0.0025 in/gu or 0.0635 mm/gu
{
E(0){fill{within{sphere(0,0,0,0.250)}}}
}

