{
  "abstract": "We introduce version 5.0 of the bottom-up open-source coarse-graining software (BOCS) package. BOCS employs the force-matching variational principle to parametrize potentials for coarse-grained (CG) models directly from atomically detailed simulations. BOCS version 5.0 significantly extends previous versions by treating potentials that depend upon the local density (LD) around each particle as well as potentials that depend upon the square gradient (SG) of this local density. We also describe a new package, PKG-BOCS, for simulating these potentials with LAMMPS. This software treats complex molecular topologies and provides considerable flexibility for defining the local density as well as the LD and SG potentials. We present numerical calculations that provide physical insight into these potentials and their dependence on the definition of the local density. These calculations also demonstrate the accuracy and reliability of our implementation. Finally, we demonstrate that LD potentials can improve the structural fidelity, thermodynamic properties, and transferability of CG models for water.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Maria C. Lesniewski",
      "orcid": "0009-0002-4079-4370"
    },
    {
      "affs": [
        0
      ],
      "name": "Michael R. DeLyser"
    },
    {
      "affs": [
        0
      ],
      "name": "W. G. Noid",
      "orcid": "0000-0001-9675-8489"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bbnth5jd670xd.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jctc.6c01228",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13718548/",
  "id": "bbnth5jd670xd",
  "issns": [
    "1549-9618",
    "1549-9626"
  ],
  "landing_url": "https://doi.org/10.1021/acs.jctc.6c01228",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "heading",
      "Statistical Mechanics"
    ],
    [
      "openalex",
      "1606|Advanced Physical and Chemical Molecular Interactions"
    ]
  ],
  "openalex": "W7163706943",
  "pdf_url": null,
  "pmcid": "PMC13718548",
  "pmid": "42937656",
  "published": "2026-10-12",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bbnth5jd670xd.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T12:22:33Z",
      "native_id": "PMC13718548",
      "source": "pmc",
      "url": "https://doi.org/10.1021/acs.jctc.6c01228"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1606|Advanced Physical and Chemical Molecular Interactions",
      "subfield": "physical"
    }
  ],
  "title": "Progress toward a Better BOCS: Systematic Coarse-Graining with Local Density Potentials",
  "title_text": "Progress toward a Better BOCS: Systematic Coarse-Graining with Local Density Potentials",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:33Z",
  "url": "https://research.draconitic.com/paper/bbnth5jd670xd",
  "venue": "Journal of Chemical Theory and Computation",
  "versions": []
}