An efficient O(N) algorithm has been developed on the basis of the proper integration between an internal coordinate method (ICM) and a multibody molecular method. The method has been implemented for virtual prototyping of molecular systems with a simple chain structure and the results showed O(N) computational performance. This paper results the application of O(N) procedure to a large molecular chain and show the linear computational load relationship with the number of subsets. Initially, a brief introduction to O(N) procedure and the theoretical development of the algorithm is presented. Later focus will be turned to the implementation of the algorithm on the molecular structure. Finally, the motion behavior and the simulation time are analyzed for different computer systems.

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