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alchemistry / alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal
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[review] Figure 12 #97

Closed ppxasjsm closed 4 years ago

ppxasjsm commented 4 years ago

Section 8.5 and Figure 12: Here I would again mention the use of both forward and reverse cumulative averages and plot them explicitly in Figure 12.

Is this possible to do? Is the data available? Figure.pdf

andrrizzi commented 4 years ago

I found some data that might be usable. What do you think about this? https://github.com/alchemistry/alchemical-best-practices/blob/update_fig_12/paper/figures/fig9_convergence/Figure.pdf

I have included in the plot a forward/reverse free energy trajectory for a single replicate. We could use it to show that the test can detect lack of convergence.

davidlmobley commented 4 years ago

Looks good, yes!

ppxasjsm commented 4 years ago

Great! Could the reference dashed line maybe not also be dashed? Maybe a straight one or dashed dotted or something to show that this is the reference?

andrrizzi commented 4 years ago

Maybe a straight one or dashed dotted or something to show that this is the reference?

Done! I went with the dash-dot line to make it different from the free energy trajectories. I have also updated the caption, the text in the manuscript, and the review document.

I have manually uploaded on overleaf the Figure.pdf file, but I haven't manually updated the code/data on overleaf since I suspect that will happen when it will be synched with github after the PR has been merged.

ppxasjsm commented 4 years ago

Perfect! Looks great. I'll deal with the rest. I'll leave the issue open for now, but will close when I'll be working my way through all of it next week.