A Hybrid Parallelizable Algorithm for Computer Simulation of Rigid Body Molecular Dynamics

Molecular dynamics is effective for a nano-scale phenomenon analysis. This paper presents a hybrid parallelizable algorithm for the computer simulation of the motion behavior of molecular chain and open-tree structure on parallel computing system. The algorithm is developed from an approach of rigid body dynamics, in which interbody constraints are exposed so that a system of largely independent multibody subchains is formed. The increased parallelism is obtainable through bringing interbody constraints to evidence and the explicit determination of the associated constraint forces combined with a sequential O(n) procedure. Each subchain then is assigned to a processor for parallel computing. The algorithm offers a sequential O(n) performance if there is only one processor available. The algorithm has O(log₂n) computational efficiency if there are as many processors available as number for molecular bodies. For most common scenario, the algorithm will give a computational complexity between O(n) and O(log₂n) if number of available processor is less than number of molecular bodies.