955 research outputs found
Stochastic dynamics simulations in a new generalized ensemble
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte
Carlo algorithms in the recently proposed generalized ensemble that is based on
a physically motivated realisation of Tsallis weights. The effectiveness of the
methods are tested with an energy function for a protein system. Simulations in
this generalized ensemble by the three methods are performed for a penta
peptide, Met-enkephalin. For each algorithm, it is shown that from only one
simulation run one can not only find the global-minimum-energy conformation but
also obtain probability distributions in canonical ensemble at any temperature,
which allows the calculation of any thermodynamic quantity as a function of
temperature.Comment: to appear in Chem. Phy. Let
Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem
We compare a few variants of the recently proposed multicanonical method with
the well known simulated annealing for the effectiveness in search of the
energy global minimum of a biomolecular system. For this we study in detail
Met-enkephalin, one of the simplest peptides. We show that the new method not
only outperforms simulated annealing in the search of the energy groundstate
but also provides more statistical-mechanical information about the system.Comment: to be published in Physica A, LATEX 32 pages, figures available on
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