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In the paper "DeePCG: Constructing coarse-grained models via deep neural networks", it says:

"In molecular dynamics (MD), we are often faced with two types of coarse-graining tasks.

In a first set of applications, we are interested in evaluating the Landau free energy, which is a function of a small subset of coarse-grained (CG) variables. In this case, the CG variables are either scalar or low dimensional vector variables.

In a second set of applications, we are interested in sampling with molecular dynamics (MD) or with Monte Carlo (MC) the configurations of an extensive set of CG variables."

In my opinion, the sentence:

In molecular dynamics (MD), we are often faced with two types of coarse-graining tasks.

should have been:

In molecular modeling ...

Am I correct?

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Technically, I think you are correct: if you are talking about both molecular dynamics simulations and Monte Carlo methods, then you are talking about molecular modelling.

But why not get even more technical? After all, neural network potentials are almost all interatomic. None of them are, therefore, molecular. Surely anybody who uses DeepCG is therefore not doing molecular dynamics or molecular modelling -- they are doing atomistic modelling.

Ah! But nobody actually models atoms: what they're really doing is modelling nuclear motion, with the fiction that electrons are continuously-variable point charges that just sit on top of the nuclei at all times. Very well, nobody is allowed to say "molecular dynamics", or "molecular modelling", or "atomistic simulations", or any portmanteau of components therein; what we are all really doing is point-orbitalized Born-Oppenheimer nuclear dynamics. POBOND is not a bad acronym at all!


You need to ask yourself if the precision of terminology you want to encourage (understandably!) will actually help answer a scientific question. In the context of what you are writing, will a reader make a significant mistake -- wind up with a wrong force field, or think her results have converged when they haven't -- if she mistakes "molecular dynamics" for "molecular modelling"? If yes, then you should be able to make a cogent argument for the distinction. If not, then you're distracting yourself and your readers unnecessarily.

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  • $\begingroup$ This is an excellent answer by a new user. Welcome to the site! $\endgroup$ Commented May 30, 2022 at 8:13
  • $\begingroup$ Molecular Modeling and Molecular Dynamics are two very different things. Molecular Dynamics is part of Molecular Modeling. Inside the field of Molecular Modeling you will find several techniques no related to Molecular Dynamics like DFT, semiemprirical methods, molecular docking, QSAR, ADMET, etc. etc. $\endgroup$
    – Camps
    Commented May 30, 2022 at 12:04
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From a grammatical perspective, I agree with you.

It would have been better for them to have said "in molecular dynamics calculations...". instead of just "in molecular dynamics...".

In fact, an even better sentence would be "when using molecular dynamics for molecular modeling..." and your suggestion is in this spirit.

However, every single scientific paper ever published has sentences which can be improved far more than that sentence which you singled out in your question here. Pick the paper that you think is the most perfect out of all papers, and I'll find a sentence that can be significantly improved. The improvement that you have suggested here is what most people in scientific would consider to be extremely minor, and if you point out matters like this to the authors of such papers, it might be significantly harmful to your academic career. Likewise, I am fairly certain that if I didn't edit your question (including my edit of your original title), and/or write this answer, it would have had a negative effect on your reputation as a Stack Exchange user, leading the community to take your future questions less seriously. Therefore, my advice would be for you to focus on the science. Keep in mind that every scientific paper that has ever been published, has issues like the one you found here, and hopefully knowing this will help you make better decisions on where to spend your precious time, energy and focus throughout the rest of your scientific career :)

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  • $\begingroup$ My point was - shouldn't they distinguish between MD vs. modeling/simulation? I am writing a review. Confusion is counterproductive in this case. Hence, the question. As far as I know CG can be used in both MD and MC. $\endgroup$
    – user366312
    Commented May 29, 2022 at 17:18
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    $\begingroup$ @user366312 can you please combine your last two comments into one comment? It's unfortunately too late for you to combine them with the first comment, due to the 5 minute limit, but if I saw this 2 minutes earlier I would have suggested for you to combine that one too! As for your follow-up question, this is exactly the type of road that my answer is advising you to avoid. The fact that you're asking this question in the context of wanting to write a better review is important enough that I wish you told us that in the original question. But, I still don't know how to help you/why it matters. $\endgroup$ Commented May 29, 2022 at 17:28
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    $\begingroup$ @NikeDattani wise words. Thanks. $\endgroup$
    – Sha
    Commented May 29, 2022 at 18:26
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I disagree. Generally the term "molecular dynamics" (MD) is used of a particular kind of simulation, to wit the kind where you model the forces that act on atoms and then calculate their movement. To me, "molecular modeling" sounds like a less specific term. It could refer to e.g. calculating the electronic structure of a molecule (say with DFT) without modeling the movement of atoms.

I'd say it's better to use MD because it's an established term even if it's not the most descriptive.

EDIT: I might add that you can say e.g. "molecular dynamics simulation" if you want to make it extra clear that you are talking about modeling/simulation.

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    $\begingroup$ I completely agree with you: Molecular Dynamic is a subset of Molecular Modeling. $\endgroup$
    – Camps
    Commented May 30, 2022 at 12:05

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