I am in need of progamming help and am having trouble finding resources online.
Although I am not making a game, I believe that this is the kind of problem an experienced game programmer would be able to help me solve.
I have motionless particle systems such as the following:

Where I have the coordinates of each point. I need to find out whether these systems are intersecting ([orange/blue] are, where as [orange/red] and [blue/red] are not).
There are two ways I believe this can be done:
1) Attempt to place a plane between the two sets and see if they are (almost) entirely on opposite sides.
or
2) Build a convex hull around each set and calculate the distance between the closest faces.
I am skeptical about using bounding boxes because the systems can have awkward and unpredictable shapes.
What are your thoughts on this? Which method would be the easiest to implement? Where can I find a good resource for this?
I am programming in perl, but I am familiar with C/C++/PHP/Java.
Thanks ahead of time,
-Thomas