{"id":31844644,"url":"https://github.com/bbye98/gcme","last_synced_at":"2025-10-12T07:46:46.761Z","repository":{"id":239118128,"uuid":"798522531","full_name":"bbye98/gcme","owner":"bbye98","description":"Source code for journal article \"GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems\" by Benjamin Ye, Shensheng Chen, and Zhen-Gang Wang","archived":false,"fork":false,"pushed_at":"2024-07-12T07:50:44.000Z","size":751,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-09T14:08:59.906Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://arxiv.org/abs/2403.08148","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bbye98.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-05-10T00:22:03.000Z","updated_at":"2025-02-16T21:38:07.000Z","dependencies_parsed_at":"2024-07-12T09:03:42.673Z","dependency_job_id":"90cba8ab-cfdb-4284-8ea9-40d8563cf8df","html_url":"https://github.com/bbye98/gcme","commit_stats":null,"previous_names":["bbye98/gcme"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bbye98/gcme","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbye98%2Fgcme","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbye98%2Fgcme/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbye98%2Fgcme/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbye98%2Fgcme/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bbye98","download_url":"https://codeload.github.com/bbye98/gcme/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbye98%2Fgcme/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279010675,"owners_count":26084785,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-12T02:00:06.719Z","response_time":53,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-10-12T07:46:42.123Z","updated_at":"2025-10-12T07:46:46.754Z","avatar_url":"https://github.com/bbye98.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gaussian core model with smeared electrostatics (GCMe)\n\nThis repository contains the code used in the journal article\n\n\u003e Ye, B. B.; Chen, S.; Wang, Z.-G. GCMe: Efficient Implementation of Gaussian\nCore Model with Smeared Electrostatic Interactions for Molecular Dynamics\nSimulations of Soft Matter Systems. **2024**.\nhttps://doi.org/10.48550/ARXIV.2403.08148.\n\n### Pre-requisites\n\nThe Python scripts require\n\n* [Python](https://www.python.org/downloads/)\n3.9 or later,\n* [OpenMM](\nhttp://docs.openmm.org/latest/userguide/application/01_getting_started.html),\n* [MDCraft](https://github.com/bbye98/mdcraft) 1.1 or later and its\ndependencies, and\n* either [`constvplugin`](https://github.com/scychon/openmm_constV) or\n[`openmm-ic-plugin`](\nhttps://github.com/bbye98/mdcraft/tree/main/lib/openmm-ic-plugin)\n\nto be installed.\n\nThe LAMMPS scripts have been tested to run on the 21 Nov 2023 release\nwith the `fix imagecharges` command from [`lammps-fix-imagecharges`](\nhttps://github.com/bbye98/mdcraft/tree/main/lib/lammps-fix-imagecharges).\nOlder LAMMPS builds will likely have to use the `fix imagecharges`\ncommand from [`lammps-fixes`](https://github.com/kdwelle/lammps-fixes)\ninstead due to recent internal LAMMPS API changes.\n\n### Directory\n\n    ├── benchmark\n    │   ├── ljcoul_ic_real.lmp      # LAMMPS: WCA/Coulomb system w/ image charges\n    │   ├── ljcoul_slab_real.lmp    # LAMMPS: Slab WCA/Coulomb system\n    │   ├── ljcoul_ic.py            # OpenMM: WCA/Coulomb system w/ image charges\n    │   ├── gcme_bulk_real.lmp      # LAMMPS: Bulk GCMe system\n    │   ├── gcme_ic_real.lmp        # LAMMPS: GCMe system w/ image charges\n    │   ├── gcme_slab_real.lmp      # LAMMPS: Slab GCMe system\n    │   └── gcme_all.py             # OpenMM: GCMe systems w/ all three BCs\n    ├── analysis_gcme.ipynb\n    ├── npt_water.py\n    ├── nvt_polyanion_counterion_solvent.py\n    └── nvt_water.py\n\nThe `benchmark` directory contains scripts to run simulations of simple\ncoarse-grained systems for the benchmark results in the \"Performance\"\nsection of the paper.\n\nThe `npt_water.py` script runs NpT simulations of coarse-grained \"water\"\nparticles at different pressures and repulsion parameters to determine\nthe key GCMe parametrization relationship in the \"Parametrization\"\nsection of the paper. The `nvt_water.py` script runs NVT simulations of\nthe parametrized GCM so that the most probable pair separation distance\ncan be determined using the radial distribution function.\n\nThe `nvt_polyanion_counterion_solvent.py` script runs NVT simulations of\npolyanions, their counterions, and solvent particles confined between\ntwo planar perfectly conducting or nonmetal electrodes using OpenMM as\npart of the \"Illustrative examples\" section of the paper.\n\nThe `analysis_gcme.ipynb` Jupyter notebook analyzes and plots all\nequations and simulation data included in the paper.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbye98%2Fgcme","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbbye98%2Fgcme","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbye98%2Fgcme/lists"}