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If I typed "1000" into an "Iterations" field, I would know why.
And while one of my favorite sayings is: "You can't fix stupid," I think you could put a small disclaimer up saying something like, "Warning: A large Iterations value will take longer to calculate." That really SHOULD address other concerns. Default value for the field could still be 50. Heck, it could even reset to 50 after every simulation.
I agree, but I think a better solution may be to set the iteration value to 100 after 200 simulations. I really don't like to add another input field to the form. The simulator shall stay simple and be easy to use.