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Published September 17, 2024 | Version 2.4.0
Software Open

alchemlyb

Creators

  • 1. Datryllic LLC
  • 2. Kenney Consulting, LLC
  • 3. Arizona State University
  • 4. Silicon Therapeutics LLC
  • 5. Differentiated Therapeutics
  • 6. Freie Universität Berlin
  • 7. University of California Irvine
  • 8. Pacific Northwest National Laboratory
  • 9. Wayne State University
  • 10. Exscientia plc
  • 11. University of Colorado Boulder
  • 12. University of Stuttgart
  • 13. CNRS
  • 14. University of Pennsylvania
  • 15. Open Molecular Software Foundation
  • 16. PM Scientific Consulting
  • 17. University of Trieste
  • 18. Max-Planck-Institut for Sustainable Materials
  • 19. University of North Carolina
  • 20. City University of New York
  • 21. National Institute of Standards and Technology

Description

alchemlyb is an open-source Python software package for the analysis of alchemical free energy calculations. Its functionality contains individual composable building blocks for all aspects of a full typical free energy analysis workflow, starting with the extraction of raw data from the output of diverse molecular simulation packages, moving on to data preprocessing tasks such as decorrelation of time series, using various estimators to derive free energy estimates from simulation samples, and finally providing quality analysis tools for data convergence checking and visualization. alchemlyb also contains high-level end-to-end workflows that combine multiple building blocks into a user-friendly analysis pipeline from the initial data input stage to the final results.

Notes

If you use this software, please cite it using the preferred citation together with any other references.

Files

alchemistry/alchemlyb-2.4.0.zip

Files (370.3 kB)

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md5:902402c186448b27bcd0011cbd7ce140
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Additional details

Related works

Is supplement to
Software: https://github.com/alchemistry/alchemlyb/tree/2.4.0 (URL)