dorsal/arxiv
View SchemaStochastic dynamics simulations in a new generalized ensemble
| Authors | Ulrich H. E. Hansmann, Frank Eisenmenger, Yuko Okamoto |
|---|---|
| Categories | |
| ArXiv ID | physics/9810052 |
| URL | https://arxiv.org/abs/physics/9810052 |
| DOI | 10.1016/S0009-2614(98)01148-8 |
Abstract
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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"abstract": "We develop a formulation for molecular dynamics, Langevin, and hybrid Monte\nCarlo algorithms in the recently proposed generalized ensemble that is based on\na physically motivated realisation of Tsallis weights. The effectiveness of the\nmethods are tested with an energy function for a protein system. Simulations in\nthis generalized ensemble by the three methods are performed for a penta\npeptide, Met-enkephalin. For each algorithm, it is shown that from only one\nsimulation run one can not only find the global-minimum-energy conformation but\nalso obtain probability distributions in canonical ensemble at any temperature,\nwhich allows the calculation of any thermodynamic quantity as a function of\ntemperature.",
"arxiv_id": "physics/9810052",
"authors": [
"Ulrich H. E. Hansmann",
"Frank Eisenmenger",
"Yuko Okamoto"
],
"categories": [
"physics.bio-ph",
"q-bio"
],
"doi": "10.1016/S0009-2614(98)01148-8",
"title": "Stochastic dynamics simulations in a new generalized ensemble",
"url": "https://arxiv.org/abs/physics/9810052"
},
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