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orbeckst committed Dec 29, 2021
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43 changes: 31 additions & 12 deletions README.rst
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Expand Up @@ -11,15 +11,41 @@ includes:
molecular dynamics engines such as `GROMACS`_, `AMBER`_, `NAMD`_
and `other simulation codes`_.

2. Subsamplers for obtaining uncorrelated samples from timeseries data.
2. Subsamplers for obtaining uncorrelated samples from timeseries data
(including extracting independent, equilibrated samples
[Chodera2016]_ as implemented in the pymbar_ package).

3. Estimators for obtaining free energies directly from this data, using
best-practices approaches for multistate Bennett acceptance ratio (MBAR)
[Shirts2008]_ and thermodynamic integration (TI).
[Shirts2008]_ and BAR (from pymbar_) and thermodynamic integration (TI).

In particular, it uses internally the excellent `pymbar
<http://pymbar.readthedocs.io/>`_ library for performing MBAR and extracting
independent, equilibrated samples [Chodera2016]_.
.. _GROMACS: http://www.gromacs.org/
.. _AMBER: http://ambermd.org/
.. _NAMD: http://www.ks.uiuc.edu/Research/namd/
.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html
.. _`pymbar`: http://pymbar.readthedocs.io/


Getting involved
----------------

Contributions of all kinds are very welcome.

If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_.

If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_.

We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.

.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions
.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide
.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues
.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb



References
----------

.. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal
analysis of samples from multiple equilibrium states. The Journal of Chemical
Expand All @@ -29,14 +55,7 @@ independent, equilibrated samples [Chodera2016]_.
Equilibration Detection in Molecular Simulations. Journal of Chemical Theory
and Computation 12, 1799–1805.
.. _GROMACS: http://www.gromacs.org/
.. _AMBER: http://ambermd.org/

.. _NAMD: http://www.ks.uiuc.edu/Research/namd/

.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html

.. |doi| image:: https://zenodo.org/badge/68669096.svg
:alt: Zenodo DOI
:scale: 100%
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13 changes: 10 additions & 3 deletions docs/index.rst
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Expand Up @@ -54,10 +54,17 @@ The pandas_ package (one of our other primary dependencies) also follows `NEP 29

.. _contact:

Contributing
------------
Contributions are very welcome. If you have bug reports or feature requests or questions then please get in touch with us through the `Issue Tracker`_. We also welcome code contributions: have a look at our `Developer Guide`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.
Getting involved
----------------
Contributions of all kinds are very welcome.

If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_.

If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_.

We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.

.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions
.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide
.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues
.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb
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