Typo/grammar fixes/clarity issues to deal with for revisions

[davidlmobley]

From @vtlim in my group; we should add an acknowledgment/contributions spot for her when we fix these:

• p.5, left column, bottom, "The rate coefficient kab..." is not a complete sentence. I think the word "which" here is superfluous.
• p.6, left column, end of first paragraph, two periods after "e.g."
• p.8, right column, there should be a period before the sentence "Coulombic interactions, including..."
• p.13, left column, missing the word "Figure" in the sentence "The schematic below..."
• p.15, right column, simple velocity rescaling paragraph, there's a typo that says "sample velocity rescaling"
• p.16, right column, there are unnecessary parentheses around "Table 1"
• p.16, right column, typo on the word simulations in the sentence "Such conditions correspond to..."
• p.17, left column, the sentence starting with "These impacts from" took me a few re-reads to comprehend.
• p.19, left column sentence starting with "More subtly" reads kind of odd
• p.20, right column, I'm not sure what "order of operations" is referring to
• p.20, right column, The sentence starting with "Second, even" uses the word "even" twice and is a bit confusing
• p.21, left column, the sentence starting with "Unlike the original" mentions figure 6 twice maybe redundantly
• p.23, the second heading should say "make critical decisions OF/FOR/ABOUT the system" (missing preposition)

Some general concepts that I didn't understand very well but maybe need to do my own reading, are:

• what it means for entropy to quantify the width of the basin (p.6) (Resolved by Improve discussion of entropy, charge screening #90 )
• what the reason is for reducing 1-4 interactions (p.8)
• many simulations use the Hamiltonian formulation but via the Newtonian eqns of motion? (p.3,15) (DLM: Seems outside of scope.)
• why the opposite sign screening function is used for direct space in Ewald summation (p.21) (Resolved by Improve discussion of entropy, charge screening #90)

[hmayes]

I have some time to make changes today; will make a pull request when I'm done

[hmayes]

Items from the review that I have not yet addressed:

• P. 2, col. 2, top: "I don't see why this is particular to free-energy calculations, and not, say, transport properties."

• P. 3, col. 2, bottom: This sentence was highlighted with no explanation: "These concepts
  play an important role in development and proper implementation of simulation methods. For example, a particularly straightforward check of the correctness of an MD code is to test whether energy is conserved." (DLM: I don't see how to fix this one since the sentence reads fine to me. So we'll need to not do this for now.)

• P. 5, top list: do we want to add https://www.wiley.com/en-us/Thermodynamics+and+an+Introduction+to+Thermostatistics%2C+2nd+Edition-p-9780471862567? I haven't read it so I want another opinion before adding (DLM: I haven't read it and it is expensive; I'd want an endorsement from someone we know before adding it.)

• p. 11, 2nd column, last sentence the reviewer added "Although outside the stated scope, a specific example here could be helpful. Perhaps one showing a large molecule with different types of carbon atoms having different force-field parameter assignments." (DLM: Won't address, outside of scope.)

• p. 12, first column, middle, the reviewer highlighted our sentence "Since the momentum
  of the center-of-mass of the simulation box is conserved by Newtonian dynamics, the last particle is typically assigned a velocity to guarantee that the center-of-mass momentum is zero, preventing the simulation box from drifting" and wrote: "A less risky approach is to assign the velocities and then add a constant to all of them to zero the com momentum. Otherwise that last atom could end up with an abnormally large velocity."

• p. 12, paragraph after last comment: "If many short trajectories are of interest (e.g., with transition path sampling), the velocity assignment is more important. For example, if a velocity is assigned with a component that violates a constraint (e.g., bond length), it will be zeroed out, potentially leading to a subtle systematic error."

• p. 16, col 1, last sentence of "Langevin"--reviewer wrote "Wouldn't zero dampling reduce to the Andersen thermostat, due to F_random?" (DLM: The answer is no, see below. We clarified in the text.)

• p. 17, col 1, end of paragraph starting "For the purpose..." the reviewer wrote "Something should be said about what is meant by "scaling", and how molecules are moved when the volume changed."

• p. 20, col 1, 2/3 down, by the sentence "Some examples of these enhanced timestepping algorithms...", the reviewer wrote: "One should also ensure that the averages don't change (distinct from drift) with time step, particular when using a thermostat."

• p. 21, Figure 7: "This could be a bit misleading in that the screened interactions start at a lower value at r = 1. The vdW line I assume has an arbitrary scale, so there's no need from them to start from different points." (Done)

• p. 23, 2nd checkmark: "It is not advisable to do mu-P-T simulations. " (DLM: Removing this from the checklist; it seems we were overambitious in listing options.) and "For mixtures, consider semigrand or osmotic ensembles too". (DLM: done, as footnote -- not mainstream yet.)

[davidlmobley]

Thanks!

[justinGilmer]

Sorry, I missed these notifications. I will work on these this afternoon/evening.

[JIMonroe]

I have checked off items that I have addressed (check boxes 5, 6, and 9) and pushed the changes to a commit in the hbmayes branch (hope that's alright).

For check box 3, I also have not read this book.

I'm voting to ignore check box 4 since we already talk about choosing force fields earlier in the document, and as the reviewer mentions, we can't possible stay within the scope while providing force field parametrization suggestions.

[hmayes]

Fine/great by me!

[davidlmobley]

Thanks, @hmayes and @JIMonroe ! I'll try and deal with more issues tonight and tomorrow.

[davidlmobley]

OK, I got Vickie's changes dealt with except the issue on "many simulations use the Hamiltonian formulation but via the Newtonian eqns of motion?", which seems outside of scope (I don't see a quick/easy explanation). Shall I strike through that one, @hmayes and @JIMonroe ?

[davidlmobley]

@EfremBraun - do you know the answer to this? "p. 16, col 1, last sentence of "Langevin"--reviewer wrote "Wouldn't zero dampling reduce to the Andersen thermostat, due to F_random?" I'm not familiar with details of how the random force is handled and whether it is exactly equivalent.

Update: Answered this myself; the answer is "no". The friction force and the random force are related by the fluctuation/dissipation theorem so the amount of each is coupled in order to retain correct properties. So this does NOT reduce to Andersen in the limit of 0 friction/noise; it just becomes constant energy Newtonian dynamics.

[davidlmobley]

@samarjeet did you create the figure on decay of electrostatic interactions? I'm not seeing code for it in this repo; we need to generate an updated version of it with a different vertical axis scale. Can you do so, or provide code to re-generate? (Ideally both!)

[samarjeet]

@davidlmobley Yes, I can update it as well as attach the code as well. Let me do that asap.