ramess101
commented
5 years ago Here are @mrshirts comments for the introduction. I have only copied those that could require some discussion (i.e., I did not include changes for referred to word choice). The marked-up PDF can be found in the Reviews_coauthors directory:
A few title issues: I think "replaces" is too strong; you can use it, it's just not as good (or maybe it IS as good in some situations). Also,I don't like MBAR in titles, since it's a little too specific. Also, I think the reweighting approach is more general for histogram-type calculations. Multistate reweighting provides a better alternative to histogram reweighting for coexistance calculations.
Is it higher precision even given the higher expense? i.e. if requires 9 times more simulations, is it at leastr 3x more precise? If not, not really more precise (though maybe more parallelizable).
These are two different things: one is error that any method needs, the other is additional analysis on top of any uncertainty analysis.
If introducing MBAR, would be good to say why it's fundamentally different. "Multistate Bennett Acceptance Ratio, which reweights individual samples rather than histograms of data. This method can be shown to have the lowest uncertainty of all reweighting methods and is readily available . . . "
I would suggest leading with what the study is instead of what it isn't.
I'd get this in earlier -- this is the main point -- that doing MBAR makes it possible to do things that aren't possible with MBAR. The reason (which you should probably try to present in the introduction) is that WHAM/HR lumps all configurations together that have the same energy; but that if you want to distinguish them in some other way (for example, you need to group them differently by the energy they have in a new state), then you want to treat each sample seperately, whic his what MBAR does.
Suggest reorganizing so that you first provide the hypothesis (GCMC-MBAR should work better than MBAR-ITIC), and then the reasons - otherwise, it's not as clear why you are giving the MBAR-ITIC information.
Would be nice of the MBAR was a both suffix/prefix in both cases, but not sure that's possible because of convention.
By the time the paper is published, it's not an aspiration, it's a finding (or a disproved hypothesis if it fails!). Should work on making language consistent; by the time the paper is read, the hypothesis will have vbeen tested. So we can test a hypotheses, but we hypothesized in the past. There are a few ways to set it up, but I would say that
I'll have to take a look at it [Hamiltonian scaling] to be able to describe the connection better.
@mrshirts @msoroush @jpotoff
I decided to keep track of the manuscript feedback on GitHub. You are welcome to respond via email because I will copy all comments to this issue tracker anyways:
I know that I just sent you the outline this morning, but I thought I would send you the manuscript as certain sections are completed. This way you can review the paper piecemeal at your convenience. Currently, I have a rough draft of the Introduction (see attached, alternatively, you can access the JCED_FOMMS_manuscript.tex file at https://github.com/ramess101/JCED_FOMMS_Manuscript).
I would especially appreciate your opinions whether you think the comparison of GEMC and GCMC-HR is necessary/helpful for the Introduction. Because Michael is our MBAR expert and Jeff and Mohammad are the GCMC-HR experts, please make sure my descriptions are accurate regarding these two fundamental aspects of the manuscript.