Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.
We propose a generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multidimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. Furthermore, from the results of the multicanonical-multioverlap molecular dynamics simulation, we obtain a local-minimum state of the Met-enkephalin system.
Itoh
Satoru G
SG
Department of Physics, School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan. itoh@tb.phys.nagoya-u.ac.jp
Okamoto
Yuko
Y
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding
D010455:Peptides