It is difficult to answer this if you don't know anything about either subject as it appears from your question. Try "molecular docking tutorial" or a similar search in Google - there are nice suggestions at the very top. Briefly, you will need to prepare molecules in proper format, and it helps if you know at least roughly where the docking site is. If you are literally allowing your ligand to dock anywhere, that will take a long time and will not be very accurate. I'd suggest you focus on docking first, as MD simulation of docked complexes is a big can of worms.