dorsal/arxiv
View SchemaDual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method to Calculate Relative Free Energy Difference in Rough Energy Landscape
| Authors | Donghong Min, Hongzhi Li, Guohui Li, Ryan Bitter-Putzer, Wei Yang |
|---|---|
| Categories | |
| ArXiv ID | physics/0605005 |
| URL | https://arxiv.org/abs/physics/0605005 |
| DOI | 10.1063/1.2715950 |
| Journal | J. Chem. Phys. 126, 144109 (2007) |
Abstract
A novel overlap histogramming method based on Dual-Topology Hamiltonian-Replica-Exchange simulation technique is presented to efficiently calculate relative free energy difference in rough energy landscape, in which multiple conformers coexist and are separated by large energy barriers. The proposed method is based on the realization that both DT-HERM exchange efficiency and confidence of free energy determination in overlap histogramming method depend on the same criteria: neighboring states' energy derivative distribution overlap. In this paper, we demonstrate this new methodology by calculating free energy difference between amino acids: Leucine and Asparagine, which is an identified chanllenging system for free energy simulations.
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"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"
},
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