Theoretical studies of transition states by the multioverlap molecular dynamics methods

The multioverlap molecular dynamics method gives a flat probability distribution in the multidimensional dihedral-angle-distance space, where the dihedral-angle distance of a configuration with respect to a reference state gives a measure for structural similarity. Hence, this method realizes a random walk among specific configurations in the multidimensional dihedral-angle-distance space at a constant temperature and explores widely in the configurational space. We applied the multioverlap molecular dynamics method to a pentapeptide, Met-enkephalin, in gas phase as a test system. Comparing the results of this method with those of the conventional canonical and multicanonical algorithms, we demonstrate its effectiveness. Furthermore, from the detailed free-energy landscape obtained from the results of the multioverlap molecular dynamics simulation, we obtain the transition state between two specific reference configurations of Met-enkephalin. We also deduce the transition pathway between the two specific reference configurations. (c) 2006 American Institute of Physics.