dorsal/arxiv
View SchemaDemonstrated convergence of the equilibrium ensemble for a fast united-residue protein model
| Authors | F. Marty Ytreberg, Svetlana Kh. Aroutiounian, Daniel M. Zuckerman |
|---|---|
| Categories | |
| ArXiv ID | physics/0703222 |
| URL | https://arxiv.org/abs/physics/0703222 |
Abstract
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can accelerate canonical all-atom sampling, but require properly distributed coarse ensembles. We therefore demonstrate that full sampling can indeed be achieved in a sufficiently simplified protein model, as verified by a recently developed convergence analysis. The model accounts for protein backbone geometry in that rigid peptide planes rotate according to atomistically defined dihedral angles, but there are only two degrees of freedom (phi and psi dihedrals) per residue. Our convergence analysis indicates that small proteins (up to 89 residues in our tests) can be simulated for more than 50 "structural decorrelation times" in less than a week on a single processor. We show that the fluctuation behavior is reasonable, as well as discussing applications, limitations, and extensions of the model.
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"abstract": "Due to the time-scale limitations of all-atom simulation of proteins, there\nhas been substantial interest in coarse-grained approaches. Some methods, like\n\"Resolution Exchange,\" [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)]\ncan accelerate canonical all-atom sampling, but require properly distributed\ncoarse ensembles. We therefore demonstrate that full sampling can indeed be\nachieved in a sufficiently simplified protein model, as verified by a recently\ndeveloped convergence analysis. The model accounts for protein backbone\ngeometry in that rigid peptide planes rotate according to atomistically defined\ndihedral angles, but there are only two degrees of freedom (phi and psi\ndihedrals) per residue. Our convergence analysis indicates that small proteins\n(up to 89 residues in our tests) can be simulated for more than 50 \"structural\ndecorrelation times\" in less than a week on a single processor. We show that\nthe fluctuation behavior is reasonable, as well as discussing applications,\nlimitations, and extensions of the model.",
"arxiv_id": "physics/0703222",
"authors": [
"F. Marty Ytreberg",
"Svetlana Kh. Aroutiounian",
"Daniel M. Zuckerman"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph",
"q-bio.BM"
],
"title": "Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model",
"url": "https://arxiv.org/abs/physics/0703222"
},
"schema_id": "dorsal/arxiv",
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"type": "Model",
"variant": "snapshot-2026-03-01",
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