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.

_{This README.md is printed from 100% recycled electrons.}