Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

Source 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 Δ t . Unless RMSD(Δ t ) has reached a stationary shape, the simulation has not yet converged.