| Title: |
alchemlyb: the simple alchemistry library |
| Authors: |
Dotson, David L.; Kenney, Ian M.; Beckstein, Oliver; Liu, Shuai; Jensen, Travis; Allen, Bryce; Wille, Dominik; Lim, Victoria; Lee, Hyungro; Barhaghi, Mohammad Soroush; Wu, Zhiyi; Hsu, Wei-Tse; Schlaich, Alexander; Hénin, Jérôme; Joseph, Thomas T.; Alibay, Irfan; Merz, Pascal T.; Marson, Domenico; Fan, Shujie; Janssen, Jan; Li, Haoxi; Carter, Helmut; Mobley, David; Shirts, Michael R.; Clark, Jennifer A. |
| Publisher Information: |
Zenodo |
| Publication Year: |
2024 |
| Collection: |
Zenodo |
| Subject Terms: |
Python; free energy; molecular dynamics; alchemistry |
| 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. ; If you use this software, please cite it using the preferred citation (JOSS DOI 10.21105/joss.06934) together with any other references. |
| Document Type: |
software |
| Language: |
unknown |
| Relation: |
https://github.com/alchemistry/alchemlyb/tree/2.4.1; https://zenodo.org/records/13799339; oai:zenodo.org:13799339; https://doi.org/10.5281/zenodo.13799339 |
| DOI: |
10.5281/zenodo.13799339 |
| Availability: |
https://doi.org/10.5281/zenodo.13799339; https://zenodo.org/records/13799339 |
| Rights: |
BSD 3-Clause "New" or "Revised" License ; bsd-3-clause ; https://opensource.org/licenses/BSD-3-Clause |
| Accession Number: |
edsbas.599EDDB4 |
| Database: |
BASE |