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MobleyLab / relative-solvation-paper

Paper on reproducibility of relative solvation free energies across packages
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Reviewer 2-Q4: Differences in perturbed groups between software #44

Closed Steboss closed 6 years ago

Steboss commented 6 years ago

Is there any difference in which atoms in the perturbed groups that are allowed to have different coordinates between the different software? It is not obvious that topologically equivalent atoms (the common substructure) should have identical coordinates, at least not for binding free energies.

davidlmobley commented 6 years ago

I am not sure about this. Do you guys know, @Steboss and @jmichel80 ?

halx commented 6 years ago

A dual topology method can indeed be dual-coordinates. But I think a single topology method implies also single-coordinate. At least the implementations we work with, are.