dorsal/arxiv
View SchemaResolution exchange simulation with incremental coarsening
| Authors | Edward Lyman, Daniel M. Zuckerman |
|---|---|
| Categories | |
| ArXiv ID | physics/0601093 |
| URL | https://arxiv.org/abs/physics/0601093 |
Abstract
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally applicable incremental coarsening procedure and apply the algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate a combination of resolution and temperature exchange, in which the coarser simulations are also at elevated temperatures. Both simulations are implemented in a ``top-down'' mode, to allow efficient allocation of CPU time among the different replicas.
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"date_created": "2026-03-02T18:01:04.285000Z",
"date_modified": "2026-03-02T18:01:04.285000Z",
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"abstract": "We previously developed an algorithm, called resolution exchange, which\nimproves canonical sampling of atomic resolution models by swapping\nconformations between high- and low-resolution simulations[1]. Here, we\ndemonstrate a generally applicable incremental coarsening procedure and apply\nthe algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate\na combination of resolution and temperature exchange, in which the coarser\nsimulations are also at elevated temperatures. Both simulations are implemented\nin a ``top-down\u0027\u0027 mode, to allow efficient allocation of CPU time among the\ndifferent replicas.",
"arxiv_id": "physics/0601093",
"authors": [
"Edward Lyman",
"Daniel M. Zuckerman"
],
"categories": [
"physics.bio-ph",
"physics.chem-ph"
],
"title": "Resolution exchange simulation with incremental coarsening",
"url": "https://arxiv.org/abs/physics/0601093"
},
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"source": {
"execution_id": "061e9018-fd83-4ac6-8d5d-f03a52c91b8d",
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"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
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