Fast far-field potential evaluation in multibody-based simulations of biopolymers

A novel algorithm to approximate the long-range potential field in multiscale simulations of biopolymers is presented. These models contain various domains including single particles, as well as regions with coarse-grained clusters in which high frequency modes of motion are suppressed. Herein, coarse-grained regions are formed via treating groups of atoms as rigid and/or flexible bodies/clusters connected together via kinematic joints, and as such, multibody dynamic techniques are used to form and solve the equations of motion. In such simulations with n particles, the evaluation of the potential field with computational complexity of O(n²), if not performed wisely, may become a bottleneck. This paper presents the approximation of the potential field due to the interaction between a charged particle and a body containing charged particles. This approximation is expressed in terms of physical and geometrical properties of the bodies such as the entire charge of the cluster and a pseudo-inertia tensor. Further, a divide-and-conquer scheme is introduced to implement the presented far-field potential evaluations. In this scheme adjacent charged bodies are combined together to form new bodies. The mathematical framework to create these new assemblies is presented. Then the potential of the resulting bodies on the charged particles which are far from them are recursively calculated.