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.

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:

pip install asyncmd

Documentation

See the asyncmd documentation for more information.

Contributing

All contributions are appreciated! Please refer to the documentation for information.

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