Metadata-Version: 2.4
Name: asyncmd
Version: 0.5.0
Summary: asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax.
Author-email: Hendrik Jung <hendrik.jung@biophys.mpg.de>
Maintainer-email: Hendrik Jung <hendrik.jung@biophys.mpg.de>
Project-URL: Documentation, https://asyncmd.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/bio-phys/asyncmd.git
Project-URL: Issues, https://github.com/bio-phys/asyncmd/issues
Keywords: molecular dynamics,molecular-dynamics,MD,high performance computing,HPC,slurm,SLURM,gromacs,GROMACS
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: aiofiles
Requires-Dist: mdanalysis
Requires-Dist: numpy
Requires-Dist: scipy
Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: myst-nb; extra == "docs"
Requires-Dist: sphinx-book-theme; extra == "docs"
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-asyncio; extra == "tests"
Provides-Extra: tests-all
Requires-Dist: asyncmd[tests]; extra == "tests-all"
Requires-Dist: h5py; extra == "tests-all"
Requires-Dist: coverage; extra == "tests-all"
Requires-Dist: pytest-cov; extra == "tests-all"
Provides-Extra: dev
Requires-Dist: asyncmd[docs,tests-all]; extra == "dev"
Requires-Dist: jupyterlab; extra == "dev"
Requires-Dist: ipywidgets; extra == "dev"
Requires-Dist: tqdm; extra == "dev"
Requires-Dist: pylint; extra == "dev"
Dynamic: license-file

# 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, <https://doi.org/10.21105/joss.08321>

## 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.

---
<sub>This README.md is printed from 100% recycled electrons.</sub>

[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
