This is very common to any circuit simulator while doing simulation with large capacitance. Supposing Hyperlynx use a 10 ps time step to simulation, it means there are 500X10 X 100 steps for your current setting. It will run very long time whatever how much memory you have.
just change time scale to 1-10ns and replace capacitor with a resistor(2πfC) or create a spice file for you capacitor with initial voltage. For detail, just go to supportnet and search an appnote "Simulating Nets With Large Series Capacitors in HyperLynx"