you can use the InterEvDock2 web interface at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/. This server is an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

or you can use RosettaDock server for local protein–protein docking

If I understand the question correctly, you want to plot a certain value for this "interaction" (angle, distance probably ?) in time. To answer this question it is important to know which MM Force Field you used for the MD simulation ?

Dear Michiel,

You were correct and the MM force field used was MEDUSA for the simulation.