Implementation of an Efficient Algorithm for Virtual Prototyping of Dynamics of Molecular Conformation

This paper presents an O(N) algorithm and its preliminary computer simulation results for virtual prototyping of molecular systems with a simple chain structure. The algorithm is based on proper integration between an internal coordinate method (ICM) and a multibody molecular model. ICM method makes the use of recursive relations possible between two adjacent subsets within a molecular system. The multibody molecular model takes the benefits of freezing degrees of freedom of some lightly excited high frequency bonds. Because these high frequency bonds would force the use of very small integration step sizes, which severely limits the time scales for virtual prototyping of dynamics of molecular conformation over long periods of time. Thus a new multiscale model and efficient algorithm is produced to increase computational efficiency for virtual prototyping of dynamical behaviors of molecular confirmation. This paper will be initially directed towards introduction of the new model and algorithm. Then attention will be turned to the implementation of the algorithm at macro scale, which can be used to demonstrate the validity of the procedure and algorithm. Final focus will be turned to the implementation of the algorithm to a simple molecular chain at micro scale. The algorithm gives an O(N) computational performance for formation/solution of equations of motion for a molecular chain system.