Restructure beginning of "What simulation protocol should I use"

[fjclark]

Proposed Change

Restructure the beginning of the "What simulation protocol should I use". In particular, remove the single/ dual topology section and begin with a more fundamental discussion which might more naturally include all of the options e.g. ATM, as suggested by @sboresch. This will likely benefit from following @egallicc's updates to the theory section (see #136).

Proposed Authors and Reviewers

Please confirm (before the end of January) that you are happy to author/ review and state when you're available. Authors, please say roughly when you plan to contribute the changes (no later than the end of May).

Proposed author: @sboresch
Proposed reviewer: Volunteer wanted

[sboresch]

I'll try my best ;-) @egallicc would be an obvious reviewer, and/or Darrin York.

[fjclark]

Thank you!

[fjclark]

@yorkdm has again confirmed that he will review the updates to the theory (#155) soon. However, if you were planning to start writing soon, please just assume that changes to the current PR will be minimal, @sboresch.

[sboresch]

I have now thought quite a bit about this section/passage, and as I mentioned in the initial discussion, I think that the established single/dual topology classification is not sufficient anymore. I have summarized my thoughts in a Google doc (https://docs.google.com/document/d/1zUgwv3HA0wJuC19nDzrrpjh4-iZVsNULKagEPFUBUq8/edit?usp=sharing)

Note: This is not a draft of how I want to rewrite Sect. 6; rather, I intend to start the discussion how to proceed here. Obviously, if there is consensus, some parts of the text I wrote will/can become part of the manuscript.

Feedback appreciated; thanks in advance.