{"id":37063339,"url":"https://github.com/bio-phys/asyncmd","last_synced_at":"2026-01-14T07:12:34.878Z","repository":{"id":163041187,"uuid":"612161559","full_name":"bio-phys/asyncmd","owner":"bio-phys","description":"asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.","archived":false,"fork":false,"pushed_at":"2025-08-19T13:33:22.000Z","size":3987,"stargazers_count":19,"open_issues_count":3,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-11-18T08:03:55.410Z","etag":null,"topics":["enhanced-sampling","molecular-dynamics","molecular-dynamics-simulation","slurm","slurm-cluster"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bio-phys.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","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":"2023-03-10T10:31:25.000Z","updated_at":"2025-09-24T08:17:09.000Z","dependencies_parsed_at":"2026-01-11T03:04:44.523Z","dependency_job_id":null,"html_url":"https://github.com/bio-phys/asyncmd","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/bio-phys/asyncmd","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fasyncmd","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fasyncmd/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fasyncmd/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fasyncmd/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio-phys","download_url":"https://codeload.github.com/bio-phys/asyncmd/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fasyncmd/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28412676,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T05:26:33.345Z","status":"ssl_error","status_checked_at":"2026-01-14T05:21:57.251Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["enhanced-sampling","molecular-dynamics","molecular-dynamics-simulation","slurm","slurm-cluster"],"created_at":"2026-01-14T07:12:34.222Z","updated_at":"2026-01-14T07:12:34.864Z","avatar_url":"https://github.com/bio-phys.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# asyncmd\n\n[![codecov][codecov-badge]][codecov-link] [![Documentation Status][rtd-badge]][rtd-link] [![PyPI][pypi-badge]][pypi-link] [![DOI][joss-badge]][joss-link]\n\nasyncmd is a library to write **concurrent** code to run and analyze molecular dynamics simulations using pythons **async/await** syntax.\nComputationally costly operations can be performed locally or submitted to a queuing system.\n\nasyncmd enables users to construct complex molecular dynamics (MD) workflows or develop and implement trajectory based enhanced sampling methods with the following key features:\n\n- flexible, programmatic and parallel setup, control, and analysis of an arbitrary number of MD simulations\n- dictionary-like interface to the MD parameters\n- parallelized application of user defined (python) functions on trajectories (including the automatic caching of calculated values)\n- propagation of MD until any or all user-supplied conditions are fulfilled on the trajectory\n- extract molecular configurations from trajectories to (re)start an arbitrary number of MD simulations from it\n\n**If you use asyncmd in published research please consider citing it as:**\n\n- Hendrik Jung and Gerhard Hummer, (2025). asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems. Journal of Open Source Software, 10(112), 8321, \u003chttps://doi.org/10.21105/joss.08321\u003e\n\n## Installation\n\nThe following command will install asyncmd from [PyPi][pypi-link]:\n\n```bash\npip install asyncmd\n```\n\n## Documentation\n\nSee the [asyncmd documentation][rtd-link] for more information.\n\n## Contributing\n\nAll contributions are appreciated! Please refer to the [documentation][rtd-link] for information.\n\n---\n\u003csub\u003eThis README.md is printed from 100% recycled electrons.\u003c/sub\u003e\n\n[codecov-link]: https://app.codecov.io/gh/bio-phys/asyncmd\n[codecov-badge]: https://img.shields.io/codecov/c/github/bio-phys/asyncmd\n\n[rtd-link]: https://asyncmd.readthedocs.io/en/latest/\n[rtd-badge]: https://readthedocs.org/projects/asyncmd/badge/?version=latest\n\n[pypi-link]: https://pypi.org/project/asyncmd/\n[pypi-badge]: https://img.shields.io/pypi/v/asyncmd\n\n[joss-link]: https://doi.org/10.21105/joss.08321\n[joss-badge]: https://joss.theoj.org/papers/10.21105/joss.08321/status.svg\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fasyncmd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio-phys%2Fasyncmd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fasyncmd/lists"}