halx
commented
7 years ago There are various issues with this at the moment. There are an awful lot of files and scripts in figures/sire-scripts and I do not know what they are good for. You will need to make sure that the PDFs to be included in the main text and the SI are being created automatically with the build/compile process of the document. It looks like you have there some PNG pixel map files. Please, don't! All graphics must be vector graphics to ensure high quality figures.
Steboss
I added more explanations for the Methods section and re-wrote the results section, stating Sire/SOMD best protocols, what not to do and a comparison between software There are some little notes all over the Sire/SOMD result section, since I think there are many point we should all discuss
I have updated also the SI, adding the Sire part. I have added a table with all the results obtained with the best protocol (table S4) , a table comparing relative free energy of hydration computed with different constraints (table S5). Additionally, I have created a figure to compare DDG from allbonds constraints (relative vs absolute results - figure S4) and a figure with a relative free energy comparison between constraints (figure S5)
I have added cross reference package in the reprod.tex adding the Supplementary Information tex Finally, in the bibliography I have added two new papers: 1) Pearlman, David A., and Peter A. Kollman. "The overlooked bond‐stretching contribution in free energy perturbation calculations." The Journal of chemical physics 94.6 (1991): 4532-4545.
tex keyword: pearlman1991overlooked
2) Hopkins, Chad W., et al. "Long-time-step molecular dynamics through hydrogen mass repartitioning." Journal of chemical theory and computation 11.4 (2015): 1864-1874.
tex keyword: hopkins2015long