{
  "annotation_id": "094e8279-39f1-4c09-8efd-f0b641882ba3",
  "date_created": "2026-03-02T18:01:07.646000Z",
  "date_modified": "2026-03-02T18:01:07.646000Z",
  "file_hash": "28e8cb7eb0c87782a9a57cdbe8fab8386ef1ce4017bf7ce9562896d7c147dc7e",
  "private": false,
  "record": {
    "abstract": "A novel overlap histogramming method based on Dual-Topology\nHamiltonian-Replica-Exchange simulation technique is presented to efficiently\ncalculate relative free energy difference in rough energy landscape, in which\nmultiple conformers coexist and are separated by large energy barriers. The\nproposed method is based on the realization that both DT-HERM exchange\nefficiency and confidence of free energy determination in overlap histogramming\nmethod depend on the same criteria: neighboring states\u0027 energy derivative\ndistribution overlap. In this paper, we demonstrate this new methodology by\ncalculating free energy difference between amino acids: Leucine and Asparagine,\nwhich is an identified chanllenging system for free energy simulations.",
    "arxiv_id": "physics/0605005",
    "authors": [
      "Donghong Min",
      "Hongzhi Li",
      "Guohui Li",
      "Ryan Bitter-Putzer",
      "Wei Yang"
    ],
    "categories": [
      "physics.chem-ph"
    ],
    "doi": "10.1063/1.2715950",
    "journal_ref": "J. Chem. Phys. 126, 144109 (2007)",
    "title": "Dual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method   to Calculate Relative Free Energy Difference in Rough Energy Landscape",
    "url": "https://arxiv.org/abs/physics/0605005"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "28155349-b491-4353-8e25-b7fa1f81d014",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}