{
  "id": "0707.3382",
  "version": "v1",
  "published": "2007-07-23T13:42:24.000Z",
  "updated": "2007-07-23T13:42:24.000Z",
  "title": "Generalized-Ensemble Algorithms for Protein Folding Simulations",
  "authors": [
    "Yuji Sugita",
    "Ayori Mitsutake",
    "Yuko Okamoto"
  ],
  "comment": "37 pages, (LaTeX2e), 5 figures",
  "categories": [
    "cond-mat.stat-mech",
    "cond-mat.soft"
  ],
  "abstract": "Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other parameter space. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review the generalized-ensemble algorithms. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present further extensions of the above three methods.",
  "revisions": [
    {
      "version": "v1",
      "updated": "2007-07-23T13:42:24.000Z"
    }
  ],
  "analyses": {
    "keywords": [
      "protein folding simulations",
      "generalized-ensemble algorithms",
      "molecular dynamics versions",
      "potential energy space",
      "monte carlo"
    ],
    "publication": {
      "journal": "Rugged Free Energy Landscape,s",
      "year": 2008,
      "volume": 736,
      "pages": 369
    },
    "note": {
      "typesetting": "LaTeX",
      "pages": 37,
      "language": "en",
      "license": "arXiv",
      "status": "editable",
      "adsabs": "2008LNP...736..369S"
    }
  }
}