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The usual reason that a larger size air handler will tend to show more of the dreaded SimHVAC: Maximum Iterations warnings is because with the larger system the terminal units spend more time running at the minimum stop on the VAV damper. A common situation for getting these warnings is during times of low load when loads are just starting to pick up and the dampers begin to ramp up from the minimum stop. If you can diagnose that these errors are occuring during such times, by studying detailed frequency time series results, then I believe it is safe to ignore them. What usually happens is that when the damper varies, both the flow and supply air temperature are changing at the same time and the air system solver doesn't settle into one solution. The supply deck temperature changes because of economizer action as the ratio of outdoor to return air changes with variations in overall flow. This has been a long standing problem with no easy solution.