{"id":26366220,"url":"https://github.com/ankhoa1212/molecular-dynamics-simulation","last_synced_at":"2026-02-08T02:40:04.249Z","repository":{"id":282483756,"uuid":"940274166","full_name":"ankhoa1212/molecular-dynamics-simulation","owner":"ankhoa1212","description":"This project uses LAMMPS to simulate molecular dynamics","archived":false,"fork":false,"pushed_at":"2025-07-25T22:28:10.000Z","size":45760,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-26T05:57:04.323Z","etag":null,"topics":["bash-scripting","cplusplus","docker","lammps","molecular-dynamics-simulation","python3"],"latest_commit_sha":null,"homepage":"","language":"Python","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/ankhoa1212.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}},"created_at":"2025-02-27T22:35:23.000Z","updated_at":"2025-07-25T22:28:13.000Z","dependencies_parsed_at":"2025-03-14T23:24:58.479Z","dependency_job_id":"ec3f2866-2db7-48a1-8821-fef7a08f6d20","html_url":"https://github.com/ankhoa1212/molecular-dynamics-simulation","commit_stats":null,"previous_names":["ankhoa1212/molecular-dynamics-simulation"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ankhoa1212/molecular-dynamics-simulation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ankhoa1212%2Fmolecular-dynamics-simulation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ankhoa1212%2Fmolecular-dynamics-simulation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ankhoa1212%2Fmolecular-dynamics-simulation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ankhoa1212%2Fmolecular-dynamics-simulation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ankhoa1212","download_url":"https://codeload.github.com/ankhoa1212/molecular-dynamics-simulation/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ankhoa1212%2Fmolecular-dynamics-simulation/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268254118,"owners_count":24220753,"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":"2025-08-01T02:00:08.611Z","response_time":67,"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":["bash-scripting","cplusplus","docker","lammps","molecular-dynamics-simulation","python3"],"created_at":"2025-03-16T20:15:49.509Z","updated_at":"2026-02-08T02:40:04.203Z","avatar_url":"https://github.com/ankhoa1212.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# molecular-dynamics-simulation\nThis project uses LAMMPS to simulate molecular dynamics.\n\n## Linux Setup\n[Install](https://docs.lammps.org/Install.html) and [Build](https://docs.lammps.org/Build.html) LAMMPS.\n\n### Temporary Environment Variable Setup\nUse the following to set up env variables in the commandline to run the ```lmp``` command (first navigate to the directory of the executable):\n\n```\nEXECUTABLE_DIR=$PWD\n```\n\n```\nexport PATH=$EXECUTABLE_DIR:$PATH\n```\n\n### Bash Shell Environment Variable Setup\nAdd the following to the ```~/.bashrc``` file (replace ```/path/to/dir``` with the path to the directory of the executable):\n\n```\nexport PATH=/path/to/dir:$PATH\n```\n\n#### Setup Ovito\n\nIf on an old Linux Ubuntu version less than 22.04 that does not have ```qt.qpa.plugin 6.5.0``` may need to install ```libxcb-cursor0```\n\n## Docker Setup (Work in progress)\n[Install](https://www.docker.com/get-started/) Docker.\n\nPull docker image:\n```\ndocker pull ankhoa1212/lammps-simulations:latest\n```\n\n## Resources\n- [LAMMPS Manual](https://docs.lammps.org/Manual.html)\n  - [Installation](https://docs.lammps.org/Install.html)\n  - [Examples](https://docs.lammps.org/Examples.html)\n  - [Processing Tools](https://docs.lammps.org/Tools.html)\n  - [Library Interfaces](https://docs.lammps.org/Library.html)\n  - [Modifying and extending LAMMPS](https://docs.lammps.org/Modify.html)\n- [Light-Responsive Assembly](https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02301)\n- [Molecular Dynamics Simulation of Active Particles Video](https://www.youtube.com/watch?v=wsM2kUB6XU4\u0026ab_channel=SoftMatterLab)\n- [Molecular Dynamics Simulation of Active Particles (Brownian Motion)](https://arxiv.org/abs/2102.10399)\n- [OVITO (for Visualization)](https://www.ovito.org/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fankhoa1212%2Fmolecular-dynamics-simulation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fankhoa1212%2Fmolecular-dynamics-simulation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fankhoa1212%2Fmolecular-dynamics-simulation/lists"}