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alchemistry / alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal
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[Fig: perturbation network] Review #53

Closed ppxasjsm closed 4 years ago

ppxasjsm commented 4 years ago

I added an additional figure to the paper today showing two types of perturbation networks with @JenkeScheen help. At the moment it is quite plane looking. Should chemical structures or cycle closures or the like be added for ease of discussion in the analysis section?

Figure.pdf

davidlmobley commented 4 years ago

Yes, if it were me I'd put a 2D structure inside each bubble, and probably also build in some cycle closure stuff.

Might also be worth citing (in the paper) recent work on improved layouts of chemical graphs, e.g.

I heard that Chemical Computing Group was also doing stuff in this space (A-optimal and D-optimal graphs) but I am not offhand finding that with Google Scholar. I think it's bked into CCG's AMBER-TI thing.

ppxasjsm commented 4 years ago

I added structures and cycles etc. here 959cd5d0a75b82d714541a121a12b636f2721b4b.

Will add the additional citations.