title: Relaxation estimation of RMSD in molecular dynamics immunosimulations.
abstract: Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.
authors.affiliation: Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics, and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schreiner
authors.forename: Rudolf
authors.initials: R
authors.lastname: Karch
authors.forename: Bernhard
authors.initials: B
authors.lastname: Knapp
authors.forename: Nevena
authors.initials: N
authors.lastname: Ilieva
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D007107:Immune System / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry; D015203:Reproducibility of Results; D013997:Time Factors
chemical_list: D011506:Proteins; D011948:Receptors, Antigen, T-Cell