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.
Itoh
Satoru G
SG
Department of Physics, School of Science, Nagoya University, Aichi 464-8602, Japan. itoh@tb.phys.nagoya-u.ac.jp
Okamoto
Yuko
Y
D000465:Algorithms; D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry*; D005740:Gases; D008958:Models, Molecular; D008962:Models, Theoretical; D018377:Neurotransmitter Agents / Q000737:chemistry*; D013816:Thermodynamics
D005740:Gases; D018377:Neurotransmitter Agents; D004744:Enkephalin, Methionine