Hemodialysis is a process to clean the metabolic wastes inside human body. Our previous researches on this topic fundamentally used contemporary numerical methods (such as CFD (computational fluid dynamics), MD (molecular dynamics), etc.) to study the ultra-filtration properties and made several progresses. However, our step-forward MD study on amino-acid leaking problem which natively exists during the hemodialysis process makes the numeral calculations more complicated. To control the heavy computation load during MD simulation, in this paper, a novel parallel domain separation scheme is proposed and its optimization method is further discussed. The unique feature of this scheme is that it introduces fibers as well as "compute shaders" into the parallel computation architecture. And the further application of this parallel scheme could form a new concept of MD simulation.