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. 2018 Mar 23;8:5080. doi: 10.1038/s41598-018-22912-7

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Convergence of umbrella sampling (US) MD simulations. The convergence is illustrated by following the evolution of the potentials of mean force (PMF) for one of the most populated interfaces: TM12-TM12. PMFs were obtained with (A–E) a conventional US-MD approach for membrane proteins or (F,G) with an US-replica exchange molecular dynamics (REMD). The different curves in each panel represent the PMF obtained using different time window as indicted in the color legends. The US-MD were either started from a bound (A) or unbound state of the proteins. In (C) both (A) and (B) were combined using all the umbrella windows, while in (D) subsets of umbrellas were used (see Figure S4 for details of the windows used). In (E) the convergence of the mix 2 is shown. In (F and G) the proteins were initially bound.