{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T22:12:46Z","timestamp":1785276766673,"version":"3.55.0"},"update-to":[{"DOI":"10.12688\/f1000research.16715.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,8]],"date-time":"2019-03-08T00:00:00Z","timestamp":1552003200000}},{"DOI":"10.12688\/f1000research.16715.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,8]],"date-time":"2019-03-08T00:00:00Z","timestamp":1552003200000}}],"reference-count":44,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2019,3,8]],"date-time":"2019-03-08T00:00:00Z","timestamp":1552003200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003006","name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","doi-asserted-by":"publisher","award":["ETH-3417-2"],"award-info":[{"award-number":["ETH-3417-2"]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["200021-178762"],"award-info":[{"award-number":["200021-178762"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:\u00a0<\/ns4:bold>\n                    Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:\u00a0<\/ns4:bold>\n                    The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:\u00a0<\/ns4:bold>\n                    In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nos\u00e9-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusion:\u00a0<\/ns4:bold>\n                    TR schemes are not advisable to use in combination with weak coupling or Nos\u00e9-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.16715.3","type":"journal-article","created":{"date-parts":[[2019,3,8]],"date-time":"2019-03-08T04:00:23Z","timestamp":1552017623000},"page":"1745","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4732-5713","authenticated-orcid":false,"given":"Dominik","family":"Sidler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4963-4824","authenticated-orcid":false,"given":"Marc","family":"Lehner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Frasch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Crist\u00f3fol-Clough","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1893-4031","authenticated-orcid":false,"given":"Sereina","family":"Riniker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2019,3,8]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"1785-1791","DOI":"10.1002\/(SICI)1096-987X(19971115)18:14<1785::AID-JCC7>3.0.CO;2-G","article-title":"Difficulties 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Sidler","year":"2018","journal-title":"F1000Research."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T05:30:51Z","timestamp":1663047051000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,8]]},"references-count":44,"URL":"https:\/\/doi.org\/10.12688\/f1000research.16715.3","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.20224.r45443","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.20224.r45443","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,8]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.20224.r45443, Bojan Zagrovic, Daniel Braun, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria, 22 Mar 2019, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3#referee-response-45443","order":0,"name":"referee-response-45443","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.18272.r40235, Nico. F. A. van der Vegt, Eduard-Zintl-Institute of Inorganic and Physical Chemistry, TU Darmstadt, Darmstadt, Germany, 03 Dec 2018, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-1745\/v1#referee-response-40235","order":1,"name":"referee-response-40235","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Sereina Riniker<\/b>; <i>Posted: 10 Jan 2019<\/i>; We thank the reviewer for this suggestion. We have performed additional simulations with a stochastic thermostat, which show that the artifacts disappear with this thermostat (see updated Figures 2 and 3). We have adapted the figures, text and conclusions accordingly.","URL":"https:\/\/f1000research.com\/articles\/7-1745\/v3#referee-comment-4352","order":2,"name":"referee-comment-4352","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The authors gratefully acknowledge financial support by the Swiss National Science Foundation [200021-178762] and by Eidgen\u00f6ssische Technische Hochschule (ETH) Z\u00fcrich [ETH-34 17-2].","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Data associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).","order":0,"name":"copyright-info","label":"Copyright"}]}}