Metadata-Version: 2.1
Name: ensemble_md
Version: 1.0.0
Summary: A package for setting up, performing, and analyzing molecular dynamics ensembles using GROMACS
Author: Wei-Tse Hsu
Author-email: wehs7661@colorado.edu
License: MIT
Project-URL: Documentation, https://ensemble-md.readthedocs.io/
Project-URL: Source Code, https://github.com/wehs7661/ensemble_md
Keywords: molecular mechanics,free energy calculations,advanced sampling
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Platform: Windows
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows 
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: natsort
Requires-Dist: argparse
Requires-Dist: pymbar>=4.0.1
Requires-Dist: alchemlyb>=2.0.0
Requires-Dist: pyyaml
Requires-Dist: seaborn
Requires-Dist: matplotlib<=3.8.4
Requires-Dist: pyemma
Requires-Dist: mpi4py
Requires-Dist: ruptures

Ensemble Molecular Dynamics
==============================
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`ensemble_md` is a Python package that provides methods for setting up, running, and analyzing GROMACS simulation ensembles. Currently, the package implements all the necessary algorithms for running synchronous replica exchange (REX) of expanded ensembles (EE), abbreviated as REXEE, as well as its multi-topology (MT) variation, MT-REXEE. Our future work includes implementing asynchronous REXEE and other possible variations of the REXEE method. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest) and our [JCTC paper](https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c00484).

### Reference
If you use any components of the Python package `ensemble_md` or the REXEE method in your research, please cite the following paper:

Hsu, W. T., & Shirts, M. R. (2024). Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. *Journal of Chemical Theory and Computation*. doi: [10.1021/acs.jctc.4c00484](https://doi.org/10.1021/acs.jctc.4c00484)

### Copyright

Copyright (c) 2022, Wei-Tse Hsu


### Acknowledgements
 
Project based on the 
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.6.
