alchemical-best-practices
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alchemistry
Best practice document for alchemical free energy calculations going to livecoms journal
It would be useful if we could expand on the kind of data that is generated by nonequilibrium switching or cycling calculations and the analysis strategies for these.
It would be useful to add a brief discussion of the alchemical transfer method ([absolute](https://arxiv.org/abs/2101.07894) | [relative](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129)).
- Modified Figure for dual topology. - Added Inkscape's .svg file since I do not have Adobe Illustrator. - Tried unsucessfully to build the latex files but my pdf builts...
In the dual topology example shown in the right side of Figure 3, shouldn't the H atom at the top ( and the M-placeholder in the middle) be connected to...
In section 8.3, many estimators were summarized. Is it possible to also have some description on WHAM? Because WHAM was mentioned a few times in the paper (especially in the...
Hi, I believe there is a typo with the in-text reference to Figure 1, on page 6. The text refers to Fig. 1F, but I believe this should be 1E....
Great paper! Here are a few items for your consideration... page 20, 5 lines above section 7: practise-->practice page 22, second bullet: cyro-->cryo page 22, first bullet in Affinity data...
The labels on Figure 12 say OA-G6, but it's listed in the text as OA-G3. This should be reconciled!
For after our first publication, we should include some example input files in our supporting information, as per #91 : > 4/ Is that possible to include an example of...
I know this was not put in the original manuscript because it wasn't ready at the time but I think pretty soon we should consider adding it!
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Best practice document for alchemical free energy calculations going to livecoms journal