ppxasjsm
commented
4 years ago Hey,
1/ It seems Fig 9 and 12 are identical. Based on the captions, I believe Fig 9 is not the supposed figure.
Thanks for the spot. This is due to the way the arxiv submission doesn't allow pdf uploads. I'll fix this on the arxiv.
2/ Some figures are far from where they are referred in the text. (e.g., Fig 5-7). I personally feel annoying if I have to scroll up and down multiple times to check figures when I read them in the paper.
I am afraid this cannot easily be fixed due to the fact that the paper is written in LaTeX and has automatic figure placement. I can try and improve this with proofs for a published version.
3/ Is that possible to talk more about hybrid topology? Or a figure to explain how does that work? I kind of know the answer but just think people may be interested in it.
Yes! Ideally if you have a pragraph you would like to add please suggest it and a place in the document where it can go and I'll happily add it.
4/ Is that possible to include an example of the practical single/dual topology files as part of SI? As a GROMACS user I'm particularly interested in this. Maybe just for a transformation of benzene to benzyl alcohol as illustrated in Fig 3. The detailed parameters may not be necessary but it will be good to show the actual format differences between single and dual topologies. I think it will benefit people (at least GROMACS users) in learning how to perform these simulations in practice.
I like this suggestion. At the moment we don't really have a SI and the paper itself is already a monster. I'll add it to a list of ideal future improvements, but probably wont' fix it immediately.
I really like this paper as it includes so many detailed explanations and suggestions on this technique. Above are my personal feelings after reading the current version. Some may not be feasible but I hope any of these could contribute to a better version of this paper.
Thank you for all your feedback! Much appreciated.
yunhuige
mrshirts
davidlmobley
Hi,
I read the preprint on bioRxiv (https://arxiv.org/abs/2008.03067) and have following suggestions on this version:
1/ It seems Fig 9 and 12 are identical. Based on the captions, I believe Fig 9 is not the supposed figure.
2/ Some figures are far from where they are referred in the text. (e.g., Fig 5-7). I personally feel annoying if I have to scroll up and down multiple times to check figures when I read them in the paper.
3/ Is that possible to talk more about hybrid topology? Or a figure to explain how does that work? I kind of know the answer but just think people may be interested in it.
4/ Is that possible to include an example of the practical single/dual topology files as part of SI? As a GROMACS user I'm particularly interested in this. Maybe just for a transformation of benzene to benzyl alcohol as illustrated in Fig 3. The detailed parameters may not be necessary but it will be good to show the actual format differences between single and dual topologies. I think it will benefit people (at least GROMACS users) in learning how to perform these simulations in practice.
I really like this paper as it includes so many detailed explanations and suggestions on this technique. Above are my personal feelings after reading the current version. Some may not be feasible but I hope any of these could contribute to a better version of this paper.
Thank you!