https://github.com/bio-phys/asyncmd
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.
https://github.com/bio-phys/asyncmd
enhanced-sampling molecular-dynamics molecular-dynamics-simulation slurm slurm-cluster
Last synced: 5 months ago
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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.
- Host: GitHub
- URL: https://github.com/bio-phys/asyncmd
- Owner: bio-phys
- License: gpl-3.0
- Created: 2023-03-10T10:31:25.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-08-19T13:33:22.000Z (10 months ago)
- Last Synced: 2025-11-18T08:03:55.410Z (7 months ago)
- Topics: enhanced-sampling, molecular-dynamics, molecular-dynamics-simulation, slurm, slurm-cluster
- Language: Python
- Homepage:
- Size: 3.8 MB
- Stars: 19
- Watchers: 2
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# asyncmd
[![codecov][codecov-badge]][codecov-link] [![Documentation Status][rtd-badge]][rtd-link] [![PyPI][pypi-badge]][pypi-link] [![DOI][joss-badge]][joss-link]
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.
asyncmd enables users to construct complex molecular dynamics (MD) workflows or develop and implement trajectory based enhanced sampling methods with the following key features:
- flexible, programmatic and parallel setup, control, and analysis of an arbitrary number of MD simulations
- dictionary-like interface to the MD parameters
- parallelized application of user defined (python) functions on trajectories (including the automatic caching of calculated values)
- propagation of MD until any or all user-supplied conditions are fulfilled on the trajectory
- extract molecular configurations from trajectories to (re)start an arbitrary number of MD simulations from it
**If you use asyncmd in published research please consider citing it as:**
- 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,
## Installation
The following command will install asyncmd from [PyPi][pypi-link]:
```bash
pip install asyncmd
```
## Documentation
See the [asyncmd documentation][rtd-link] for more information.
## Contributing
All contributions are appreciated! Please refer to the [documentation][rtd-link] for information.
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This README.md is printed from 100% recycled electrons.
[codecov-link]: https://app.codecov.io/gh/bio-phys/asyncmd
[codecov-badge]: https://img.shields.io/codecov/c/github/bio-phys/asyncmd
[rtd-link]: https://asyncmd.readthedocs.io/en/latest/
[rtd-badge]: https://readthedocs.org/projects/asyncmd/badge/?version=latest
[pypi-link]: https://pypi.org/project/asyncmd/
[pypi-badge]: https://img.shields.io/pypi/v/asyncmd
[joss-link]: https://doi.org/10.21105/joss.08321
[joss-badge]: https://joss.theoj.org/papers/10.21105/joss.08321/status.svg