Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

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Multidimensional control systems have been the subject of much productive research over more than three decades. In contrast to standard control systems, there has been much less reported on applications where the multidimensional setting is the only possible setting for design or produces implementations that perform to at least the same level. This paper addresses the latter area where case studies focusing on control law design and evaluation, including experimental results in one case, are reported. These demonstrate that movement towards the actual deployment of multidimensional control systems is increasing.