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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 \u03b1-Replica Exchange MD (\u03b1-REMD)\u2013a 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 \u03b1-REMD.<\/jats:p>","DOI":"10.1063\/5.0241538","type":"journal-article","created":{"date-parts":[[2025,3,12]],"date-time":"2025-03-12T09:45:37Z","timestamp":1741772737000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Hamiltonian replica-exchange method \u03b1-REMD for ring spearing elimination in polymers"],"prefix":"10.1063","volume":"162","author":[{"given":"Artem Yu","family":"Kunitsyn","sequence":"first","affiliation":[{"name":"N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences 1 , 47 Leninsky prosp., Moscow 119991,","place":["Russian Federation"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5223-5651","authenticated-orcid":false,"given":"Nadezhda A.","family":"Nekrasova","sequence":"additional","affiliation":[{"name":"Independent Researcher 2"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0234-7513","authenticated-orcid":false,"given":"Nikolai V.","family":"Krivoshchapov","sequence":"additional","affiliation":[{"name":"N. D. 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