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MobleyLab / relative-solvation-paper

Paper on reproducibility of relative solvation free energies across packages
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Reviewer 2-Q8: Explain switched protocol #48

Closed Steboss closed 6 years ago

Steboss commented 6 years ago

The switched protocol needs to be somewhat better explained in the main article. If both end states involve dummy atoms the more common approach is to first zero all charges, then run the LJ perturbation and finally insert the new charges, a three-step approach, rather than the two-step approach described. This is shortly discussed on p. 35, but it should be mentioned already in the Methods section.

halx commented 6 years ago

I can't find now what the reviewer believes to see on p.35. But I think what he is referring to is the way we need to use the codes to run separate Coulomn and vdW lambdas. This has been discussed in detail in the SI.

halx commented 6 years ago

See SI for explanation. 2-step just means it can be done with 2 input files and 2 simulation runs with GROMACS.