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Flow shop scheduling, where the machines are prearranged in order that the flow of each and every of the products that are processed in them is unidirectional. In the present paper Flow shop scheduling models in two stage are well thought of. The problem is specially structured with the idea that maximum of equivalent processing time on first machine remains always less than the minimum of equivalent processing time on second machine. The intention of the study is to find the schedule which lessens the total of the waiting time of all the jobs. The time to transport jobs from first machine to second machine is considered separately and two jobs considered as a group job. An Algorithm to optimize the desired function and the program in C++ language is proposed. Numerical example by applying the algorithm proposed is solved.