For my research into rail and road intersections, I used VISSIM quite successfully. VISSIM allows for rail signaling. Train signals control logic required two types of detection per each train traversing through the network: an entry signal, called a predictor or detector actuation, when the train is first detected arriving at the designated area; and an exit signal, when the train is detected departing from the designated area. The rail signals system consists of train predictors and the rail to road signals system, in a single system. In addition, the actual rail network system also comprises of axle counter and headway separation and dwell time technology that keeps certain degrees of separation or headway between trains travelling on the same track and in the same direction at a different time. I recommend the use of VISSIM.

While certainly not free, AutoDesk includes InfraWorks, which has integrated an agent-based modeling system originally called "Commuter" and developed by Azalient. Although this is outside my area of expertise, I think this modeling software may do what you want to do. AutoDesk is free to use for academic users, I believe.