2P057 Wang-Landau Multicanonical Method for Go-model Molecular Dynamics Simulation(01C. Protein: Property)
نویسندگان
چکیده
منابع مشابه
A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding
We have performed a multicanonical molecular dynamics simulation on a simple model protein. We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers. Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb interaction and the hydrophobic interacti...
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Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations on rugged potential surfaces such as protein. However, it is notoriously difficult to estimate the multicanonical temperature effectively. Wang and Landau developed a convenient method for estimating the density of states based on a multicanonical Monte Carlo method. In their method, the density of states ...
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We present a rigorous derivation for off-lattice implementations of the so-called "random-walk" algorithm recently introduced by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)]. Originally developed for discrete systems, the algorithm samples configurations according to their inverse density of states using Monte Carlo moves; the estimate for the density of states is refined at each simulati...
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We present a method for estimating the density of states of a classical statistical model. The algorithm successfully combines the Wang-Landau flat histogram method with the N-fold way in order to improve efficiency of the original single spin flip version. We test our implementation of the Wang-Landau method with the two-dimensional nearest neighbor Ising model for which we determine the tunne...
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The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the recent work of Wust and Landau [9] [51] by introducing a lesser known replica -exchange scheme between individual WangLandau samplers, the problem of dynamical trapping (spiking in the density of states) was avoided and a...
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ژورنال
عنوان ژورنال: Seibutsu Butsuri
سال: 2013
ISSN: 0582-4052,1347-4219
DOI: 10.2142/biophys.53.s168_3