I am interested in incorporating a Lennard-Jones potential in a simulation. When the interaction only involves the same type of particle, with same characteristics, we can use reduced units, scaling the units according to the potential well. But I assume the potential well is not the same for a case with particles of different sizes. Neither the sigma parameter should remain the same in my opinion. How can I propose the units or incorporate such feature to my code?
The question can be answered theoretically, but it would be nice to have examples with real code (in Fortran, Matlab, C, or whatever language you have experience with).