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EnergyPlus reports results using the beginning of the timestep ("0:00" is for 12 AM until 1 AM). It sounds like your MATLAB code reports the end of the timestep (h=1 is for 12 AM until 1 AM). If your MATLAB code is hard-wired to run 24 hours, and you can start the MATLAB code at a specific time like 7 AM, then EnergyPlus will need to run a 2-day simulation even though you're really only interested in 24 hours of results.