What should the run duration of a HAMMER model be set to?
Generally, you would want to run a model for as long as it takes to reach equilibrium (for pressure waves to reach or approach a final steady state). Usually that will be on the order of several times the time it takes for the transient to travel from its source to the far end of the system and back (the characteristic time). You can try a couple of different times, keeping in mind that a longer run duration will take longer to compute.
Note that in some situations the model may never achieve the final steady state - you may see waves bounce back and forth without dissipation. This can happen in the absence of friction - an example is seen here. In this case you may simply need to run the transient simulation long enough to see the initial impact of the transient event, or you may need to consider using a different transient friction method with a very long duration.
How to set the initial start time for a transient run in HAMMER