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
Get started#
This section contains everything to get you started using asyncmd.
The Basics
You might also want to have a look at the example jupyter notebooks below.
User guide#
This section provides more in-depth explanations on various topics, such as the Trajectory object or the use of complex stopping criteria for MD simulations. It also includes a section on modifying and extending asyncmd for your own use-case.
Community guide#
The following section contains information on how to get help and/or report any issues encountered using asyncmd as well as how to contribute code or documentation.
Example notebooks#
This section contains example jupyter notebooks (also included in the repository) on various topics and starts with a brief description of all notebooks.
Example notebooks
Module layout
Changelog and Indices