{"paper":{"title":"Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.DC","cs.NA"],"primary_cat":"cs.CE","authors_text":"Ale\\v{s} K\\v{r}enek, Jana Paz\\'urikov\\'a, Jaroslav O\\v{l}ha, Vojt\\v{e}ch Spiwok","submitted_at":"2018-01-08T09:55:08Z","abstract_excerpt":"Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to \"push the~simulation forward\". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~perfor"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1801.02362","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}