Checklist for changes from informal reviews

[bannanc]

This is just for me to check off what still needs to be done, I think any of the discussion should happen inside their issues. Links available

• [x] reference calculations in TIP3P water
• [x] effect instead of affect on figure 1 title
• [x] use PME and reaction field for the legend in figure 1
• [x] Check signs on all solvation free energies.
• [x] Include a brief paragraph in the conclusion that addresses the large dynamic range in calculated values compared to experiment for most submissions. I will mention here that there is always a possibility that there are uncertainties in the experimental results, but I will leave it up to Bas to discuss possible problems with his measurements. (This has come up in a lot of places)
• [x] Add brief paragraph to the methods section about the "all solvent" simulation with experimental concentrations translated to number of molecules. #12
• [x] Chose a different submission number for the example plots 23 and 49 are both from Santos Martins, which is why he caught it I think. #14
• [x] Make a pdf table of pKas and state penalties for the SI #13
• [x] Add disclaimer about possible sampling problems as a source of error, probably in the conclusion. #13
• [x] Possible disclaimer in the pKa/state penalty section that we didn't do anything to calculate uncertainty for these and there is certainly could be a high uncertainty in the pKa/state penalty. #13
• [x] Double check I've cited all the SAMPL5 papers correctly in the "types of methods used" section #11
• [x] Clarify in the "best methods section" that 14 and 36 were the only other 2 in the top ten by at least 3 of the 4 metrics being considered here. #11
• [x] add citation for discussion with Andreas for the 083 tautomer (specifically mention COSMO-RS which I didn't do before) #10

I'm willing to put a prefix on that sentence with discussion with participants including Andreas Klamt... I know we were concerned about water before discussions with anyone because we had discussed it when analyzing my logP results. #10

I will mention the quantification of water in cyclohexane when I describe his method as the "winner" so that readers know they could read more about that in his paper. #10

• [ ] [low priority] Perform error analysis on molecules with only one tautomer. I don't think this would take too long, but I think it needs to come after we address reviewer issues, etc. #12

[davidlmobley]

@bannanc - not sure I understand this point:

I'm willing to put a prefix on that sentence with discussion with participants including Andreas Klamt... I know we were concerned about water before discussions with anyone because we had discussed it when analyzing my logP results.

Can you clarify?

I will mention the quantification of water in cyclohexane when I describe his method as the "winner" so that readers know they could read more about that in his paper.

Do you have the PDF of his paper so you can check that it has the detail you're thinking of? If not let me know and I'll send it. (Actually, I think it's already out in JCAMD ASAP...)

Otherwise I think it looks good.

[bannanc]

@davidlmobley I think my point about mentioning Klamt, discussion with participants made more sense in the context of issue #10 but basically, he was arguing that he was the first one to suggest water in cyclohexane might be important, but I know we discussed it before talking to anyone in the challenge because we talked about it when discussing the logP paper. He wanted credit for the idea in our paper. I most just meant I would something like "After discussion with participants, including Andreas Klamt, ..." to the beginning of the discussion about the water in cyclohexane section, although, I believe we were concerned about this affect before talking to him.

Also, I'm adding a point above, I realized in table 5 and 6 I have sign errors on the solvation free energies, I forgot to reverse it so it is currently the free energy to remove the molecule from water instead of the free energy for solvation.

[davidlmobley]

I don't think we need to add anything to give him credit for something we talked about long before talking with him. We can certainly say that we also discussed it with him.

[bannanc]

Ok, I'll mention that we discussed it with him.

[bannanc]

I will mention the quantification of water in cyclohexane when I describe his method as the "winner" so that readers know they could read more about that in his paper. #10

I was under the assumptions from Klamt's comments that he included water in cyclohexane before the challenge, but I just skimmed through his paper and read the section on quantifying water in cyclohexane. They did not do this until AFTER they got their results so I'm not going to mention it in our paper.

[davidlmobley]

Sounds good.

[bannanc]

everything but last point is addressed in pull request #20

[bannanc]

Trying to organize my github, since this paper is already published I'm closing this issue.