Computational and Mathematical Methods in Medicine
Volume 2012 (2012), Article ID 173521, 9 pages
http://dx.doi.org/10.1155/2012/173521
Research Article

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

Wolfgang Schreiner,1 Rudolf Karch,1 Bernhard Knapp,1 and Nevena Ilieva2

1Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics, and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
2Institute for Nuclear Research and Nuclear Energy (INRNE), Bulgarian Academy of Sciences, 72, Tzarigradsko Chaussee, 1784 Sofia, Bulgaria

Received 29 June 2012; Revised 1 August 2012; Accepted 7 August 2012

Academic Editor: Francesco Pappalardo

Copyright © 2012 Wolfgang Schreiner et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.