The central rigid body is indicating by R and constituent particles are shown by A in tutorial
of MD-rigid rods. If we consider the Lj interaction between R and R, A and A, R and A, we can write it in a line as:
lj.pair_coeff.set(['R', 'R'],['A', 'A'], ['R', 'A'], epsilon=1.0, sigma=1.0)
However, the command for particles LJ interaction is
lj.pair_coeff.set(['R', 'A'], ['R', 'A'], epsilon=1.0, sigma=1.0)
For me it is like there is LJ interaction between R and A. I don't know why is the ['R', 'A'] pair is repeated for a second time. How to interpret this command? Is it meaning that there is only Lj interaction between Rtype and A type? There are not Lj interaction between R types, meaning [R, R]. How about interaction between A types particles [A, A].
Thanks for any help,