alchemistry / alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal
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[review] Fig 1 inconsistency #93

Closed ppxasjsm closed 4 years ago

ppxasjsm commented 4 years ago

Figure 1: For me there is no intrinsic difference between the free energy calculations shown in panel D and F, both transformations should be performed in the bound and unbound states to obtain meaningful results, and both should be termed relative calculations (ΔΔG). Maybe it could be more clearly indicated in general if a whole molecule is decoupled and if only a part of a molecule is transformed?

JenkeScheen commented 4 years ago

I could

let me know which you want me to implement, if at all.

ppxasjsm commented 4 years ago

I like all of these suggestions! Please go ahead with them!

ppxasjsm commented 4 years ago

Thank you for the figure changes.