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asyncmd

asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems - Published in JOSS (2025)

https://github.com/bio-phys/asyncmd

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

enhanced-sampling molecular-dynamics molecular-dynamics-simulation slurm slurm-cluster
Last synced: 6 months ago · JSON representation ·

Repository

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.

Basic Info
  • Host: GitHub
  • Owner: bio-phys
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 3.8 MB
Statistics
  • Stars: 18
  • Watchers: 2
  • Forks: 4
  • Open Issues: 3
  • Releases: 4
Topics
enhanced-sampling molecular-dynamics molecular-dynamics-simulation slurm slurm-cluster
Created almost 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

asyncmd

codecov Documentation Status PyPI DOI

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:

bash 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.

Owner

  • Name: bio-phys
  • Login: bio-phys
  • Kind: organization

JOSS Publication

asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems
Published
August 14, 2025
DOI
Volume 10, Issue 112, Page 8321
Authors
Hendrik Jung ORCID
Max Planck Institute of Biophysics, Department of Theoretical Biophysics, Frankfurt am Main, Germany
Gerhard Hummer ORCID
Max Planck Institute of Biophysics, Department of Theoretical Biophysics, Frankfurt am Main, Germany, Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
Editor
Evan Spotte-Smith ORCID
Tags
python molecular dynamics molecular dynamics simulation enhanced sampling gromacs high performance computing hpc slurm biophysics chemistry
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
authors:
- family-names: Jung
  given-names: Hendrik
  orcid: "https://orcid.org/0000-0002-2159-0391"
- family-names: Hummer
  given-names: Gerhard
  orcid: "https://orcid.org/0000-0001-7768-746X"
doi: 10.5281/zenodo.16572092
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jung
    given-names: Hendrik
    orcid: "https://orcid.org/0000-0002-2159-0391"
  - family-names: Hummer
    given-names: Gerhard
    orcid: "https://orcid.org/0000-0001-7768-746X"
  date-published: 2025-08-14
  doi: 10.21105/joss.08321
  issn: 2475-9066
  issue: 112
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 8321
  title: "asyncmd: A python library to orchestrate complex molecular
    dynamics simulation campaigns on high performance computing systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.08321"
  volume: 10
title: "asyncmd: A python library to orchestrate complex molecular
  dynamics simulation campaigns on high performance computing systems"

GitHub Events

Total
  • Create event: 5
  • Issues event: 2
  • Release event: 3
  • Watch event: 9
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 24
  • Push event: 28
  • Pull request review comment event: 3
  • Pull request review event: 5
  • Pull request event: 34
  • Fork event: 1
Last Year
  • Create event: 5
  • Issues event: 2
  • Release event: 3
  • Watch event: 9
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 24
  • Push event: 28
  • Pull request review comment event: 3
  • Pull request review event: 5
  • Pull request event: 34
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 20
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 9 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.6
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 20
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.6
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hejung (4)
  • braniii (1)
Pull Request Authors
  • hejung (23)
  • MateaTuralija (3)
Top Labels
Issue Labels
good first issue (1) enhancement (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 393 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: asyncmd

asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 393 Last month
Rankings
Dependent packages count: 9.8%
Average: 32.4%
Dependent repos count: 55.1%
Maintainers (1)
hejung
Last synced: 6 months ago

Dependencies

setup.py pypi