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
The following command will install asyncmd from PyPi:
pip install asyncmdSee the asyncmd documentation for more information.
All contributions are appreciated! Please refer to the documentation for information.
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