Multi-overlap molecular dynamics methods for biomolecular systems

We propose a molecular dynamics method for the multi-overlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the overlap space at a constant temperature and explores widely in the configurational space, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We can obtain detailed information about the free-energy landscape and the transition states among any specific reference conformations at that temperature. We also introduce a multi-dimensional extension of the multi-overlap algorithm. Appling this multi-dimensional method to a penta peptide, Met-enkephalin, we demonstrate its effectiveness.