title: Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?
abstract: 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.
authors.affiliation: Department for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria. bernhard.knapp@meduniwien.ac.at
authors.forename: B
authors.initials: B
authors.lastname: Knapp
authors.forename: S
authors.initials: S
authors.lastname: Frantal
authors.forename: M
authors.initials: M
authors.lastname: Cibena
authors.forename: W
authors.initials: W
authors.lastname: Schreiner
authors.forename: P
authors.initials: P
authors.lastname: Bauer
mesh_terms: D000465:Algorithms; D015982:Bias; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D003625:Data Collection; D006801:Humans; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation / Q000592:standards* / Q000706:statistics & numerical data; D015588:Observer Variation