Fig 3. Assessing the rate of convergence in molecular simulations.

Using the CES score we used ENCORE to assess the rate of convergence in seven molecular dynamics simulations of (A) protein G and (B) ubiquitin. In each case, we compared simulations of increasing length to the full ensemble obtained after 10μs of simulation. Per definition, the similarities thus decrease to zero at 10μs, but the rate at which low-values are obtained indicates how quickly the simulations have reached a distribution of conformations that is similar to the full ensemble. For example, simulations of both proteins with Amber ff99SB-ILDN and ff99SB*-ILDN quickly drop to very low values, reflecting the fact that the ensembles obtained after a few microseconds are very similar to those obtained at the end of the simulation. In contrast, for example, simulations with OPLS continue to explore new regions of conformational space during the entire simulations.