search

GOMC-WSU / MoSDeF-dihedral-fit

MoSDeF-dihedral-fit: A simple software package to fit dihedrals via the MoSDeF software
MIT License
3 stars 5 forks source link

Any previous works? #94

Closed naik-aakash closed 1 month ago

naik-aakash commented 4 months ago

Part of JOSS review : https://github.com/openjournals/joss-reviews/issues/6970

Dear developers,

I was reading through the paper submitted on the JOSS. There was this particular line that got me wondering if there are any previous studies that highlights this specific issue mentioned?

Due to these limitations, scientists assumed that the dihedral fits were transferable with all the atom classes in the dihedral fit; however, this is not always an accurate assumption. Some of the dihedrals were only fit to the first minimum and not the entire dihedral landscape, which can lead to errors in the predicted molecular conformations.

jpotoff commented 2 months ago

We have decided to resolve this issue by deleting the paragraph at line number 74. While this is a known phenomena in the field, once getting into the literature it was clear there isn't a neat way of doing this well within the limited space of the article.

bc118 commented 1 month ago

@naik-aakash Hello! All these tasks are completed. Additional information on each task is provided on an issue created for the JOSS review, which is Issue https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/issues/101

https://github.com/GOMC-WSU/GOMC_Examples/tree/main/MoSDeF-dihedral-fit

bc118 commented 1 month ago

@naik-aakash

A new mosdef-dihedral-fit version 0.1.0 was released on GitHub and conda-forge, which contains all the review requests. Additionally, new examples are listed on the README file and are posted here

naik-aakash commented 1 month ago

Thanks @bc118 will try to have a look asap in next days 😄

bc118 commented 1 month ago

Ok, thanks! 🙏

bc118 commented 1 month ago

@naik-aakash Please be aware of this minor change which we would like to fix for the paper, which will be reflected in the MoSDeF-dihedral-fit version 0.1.1. This was an oversight in the equally contributing tag in the authorship. https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/131

The person who had the equally contributing tag n the authorship removed is the one who submitted it, and I believe he will bring it up with the editor also, and is agreement with this change.

There is no change to the code.