Hamiltonian replica-exchange method α-REMD for ring spearing elimination in polymers.

Accurate prediction of polymer properties using molecular dynamics (MD) simulations requires a properly relaxed starting structure. Polymer models built from scratch by specialized algorithms (self-avoiding random walk, Monte Carlo, etc.) are far from relaxed and, moreover, often possess a large number of structural defects: close contacts between atoms, wrong bond distances, voids, unfavorable molecular conformations or packing, etc. This is especially problematic for ring-containing polymers whose initial structures also include ring spearing (bonds passing through cycles, including benzene rings). All these defects must be eliminated before running an MD simulation to correctly predict polymer properties. Short MD simulations can be enough to remove close contacts; however, ring spearing elimination and general structure relaxation cannot be achieved this way. In this work, we propose α-Replica Exchange MD (α-REMD)-a Hamiltonian replica-exchange MD protocol that reliably eliminates ring spearing defects and performs a general relaxation of the system. Its efficiency is demonstrated on five polyethersulfones whose initial geometries contained numerous ring intersections that were completely removed by α-REMD.