{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T02:01:37Z","timestamp":1770775297228,"version":"3.50.0"},"reference-count":51,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2017,1,11]],"date-time":"2017-01-11T00:00:00Z","timestamp":1484092800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["Sonata UMO\u2010 2015\/17\/D\/ST4\/00509"],"award-info":[{"award-number":["Sonata UMO\u2010 2015\/17\/D\/ST4\/00509"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2017,3,30]]},"abstract":"<jats:p>In this article, an implementation of steered molecular dynamics (SMD) in coarse\u2010grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all\u2010atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with G\u00f8\u2010like force field, all\u2010atom force field, and experimental results. \u00a9 2017 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.24685","type":"journal-article","created":{"date-parts":[[2017,1,11]],"date-time":"2017-01-11T07:27:12Z","timestamp":1484119632000},"page":"553-562","source":"Crossref","is-referenced-by-count":20,"title":["Introduction of steered molecular dynamics into UNRES coarse\u2010grained simulations package"],"prefix":"10.1002","volume":"38","author":[{"given":"Adam K.","family":"Sieradzan","sequence":"first","affiliation":[{"name":"Faculty of Chemistry University of Gda\u0144sk Wita Stwosza 63 Gda\u0144sk 80\u2010308 Poland"}]},{"given":"Rafa\u0142","family":"Jakubowski","sequence":"additional","affiliation":[{"name":"Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University Grudziadzka 5 Torun 87\u2010100 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