A novel geometric embedding algorithm for efficiently generating dense polymer structures

A new algorithm for generating starting polymer structures for molecular si mulations (e.g., MD) in dense phase is presented. The algorithm yields stru ctures that fulfill to a large extent rotational isomeric state (RIS) proba bilities and avoid atomic overlap. The heuristic search bases on the new pa rallel-rotation (ParRot) technique. We tested the performance of the algori thm on two polymeric systems: Atomistic polyethylene and polystyrene. The a lgorithm permits to tackle the problem of packing chains into large boxes o f size up to 50 Angstrom in a couple of hours on common workstations. Moreo ver, our packing algorithm is applicable for general polymer systems. The a lgorithm requires CPU effort scaling with a power 2.8 in the chain length, and with a power 1.5 in the number of chains. (C) 2001 American Institute o f Physics.