Implementation Issues With Far Field Approximations With Multi-Resolution Biopolymer Simulations

Current strategies to simulate the dynamic behavior of large molecular systems involve either computationally expensive fully atomistic models, or lower resolution models that have been coarsened in some manner. Coarsening is nominally accomplished by grouping tightly bonded atoms that have little relative motion. Traditionally this accomplished by treating a region as pseudo-atom and connecting it to other psuedo-atoms to reproduce the system. Alternatively this can be done with a multibody-based approach characterizing the regions as rigid or flexible bodies [1]–[6].