Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.
Okumura
Hisashi
H
Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan. okumura@biomaps.rutgers.edu
D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D011336:Probability; D011487:Protein Conformation; D013997:Time Factors; D014867:Water / Q000737:chemistry
D004151:Dipeptides; D014867:Water; D000409:Alanine