Stochastic dynamics simulations in a new generalized ensemble

Details Stochastic dynamics simulations in a new generalized ensemble Stochastic dynamics simulations in a new generalized ensemble

1998-10-27

arxiv.org/abs/physics/9810052v1

Physics

Biological Physics

to appear in Chem. Phy. Lett

Scientific paper

10.1016/S0009-2614(98)01148-8

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.

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