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• Include enhanced sampling techniques to improve convergency

  Possible starting points: - https://github.com/luancarvalhomartins/PyAutoFEP

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• Treatment of charged species

  Possible implementations: - Co-alchemical ion. - Care must be taken when the ion is recharged. It should not be interacting with the solute. What we want is a neutral buffer charge. In this case some restraints may be needed. For soluble systems, a radial flat bottom restraint should do the job. In the case of membrane, we may need to add some Z restraint so the ion does not internalize in the membrane. - Co-alchemical water [10.1021/acs.jctc.8b00825](https://pubs.acs.org/doi/10.1021/acs.jctc.8b00825). - Analytical or semi-empirical corrections. Ref: - [10.1021/acs.jctc.8b00825](https://pubs.acs.org/doi/10.1021/acs.jctc.8b00825)

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• Automatic convergency detection

  It is important to add convergency detection to the calculation. Here is a good start: https://alchemlyb.readthedocs.io/en/latest/visualisation.html

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