A novel geometric embedding algorithm for efficiently generating dense polymer structures

A new algorithm for generating starting polymer structures for molecular simulations (e.g., MD) in dense phase is presented. The algorithm yields structures that fulfill to a large extent rotational isomeric state (RIS) probabilities and avoid atomic overlap. The heuristic search bases on the new parallel-rotation (ParRot) technique. We tested the performance of the algorithm on two polymeric systems: Atomistic polyethylene and polystyrene. The algorithm permits to tackle the problem of packing chains into large boxes of size up to 50 Å in a couple of hours on common workstations. Moreover, our packing algorithm is applicable for general polymer systems. The algorithm requires CPU effort scaling with a power 2.8 in the chain length, and with a power 1.5 in the number of chains.