Merge pull request #127 from jpotoff/main

Remove line 74, revise line 72

paper/paper.bib

@@ -11,6 +11,19 @@ @article{Mayne:2013
 year = {2013}
 }
 
+#FF fitting OpenFF
+@article{Horton:2022,
+author = { Horton, J.T. and Boothroyd, S. and Wagner, J. and Mitchell, J. A. and Gokey, T. and Dotson, D. L. and Kumar, P. and Ramaswamy, B. K., and Mackey M. and Chodera, J. D. and Anwar, J. and Mobley, D. L. and Cole, D. J.},
+journal = {J. Chem. Inf. Mod.},
+volume = {62},
+issue = {22},
+pages = {5622-5633},
+title = {{Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale}},
+doi = {10.1021/acs.jcim.2c01153},
+url = {https://pubs.acs.org/doi/10.1021/acs.jcim.2c01153},
+year = {2022}
+}
+
 # FF fitting MacKerell/Guvench
 @article{Guvench:2008,
 author = {Guvench, O. and MacKerell, A.D.},

paper/paper.md

@@ -69,10 +69,7 @@ The `MoSDeF-Dihedral-Fit` [@Crawford:2023b] library lets users quickly calculate
 
 While many of these Molecular Mechanics (MM) force field parameters can be transferred between force fields, such as bonds, angles, and improper dihedrals (impropers), the proper dihedrals (dihedrals) can not be easily transferred due to the different combining rules (arithmetic and geometric) and 1-4 scaling factors (i.e., between the 1st and 4th bonded atoms) that were used in the development of the original parameters [@Berthelot:1898; @Good:1970; @Lorentz:1881]. The accuracy of these dihedral parameters is critical in obtaining the correct molecular conformations and configurations, which are absolutely required for understanding and analyzing the system's microstructure and physical properties (e.g., free energies, viscosities, adsorption loading, diffusion constants, and many more).
 
-While some dihedral fitting software currently exists, they only fit the CHARMM-style force fields [@Mayne:2013], or fit the dihedral constants to the final MM and QM energies, which need to be calculated by other means [@Guvench:2008].  Therefore, the molecular simulation community needs a generalized software package that imports QM and MM files, automatically reads and organizes the QM data, calculates the MM energies, auto-corrects the dihedral fit to account for multiple instances of the dihedral, and automatically removes the unusable cosine power series combinations due to this symmetry.  The `MoSDeF-dihedral-fit` software accomplishes all this and automatically accounts for any of the common combining rules and the 1-4 scaling factors specified via the MoSDeF XML (i.e., force field) files [@Cummings:2021; @Summers:2020; @GMSO:2019; @forcefield-utilities:2022].  By allowing the user to set any other dihedral in the molecule to zero, this software avoids forcing one dihedral fit to correct the inaccurate forces of another dihedral, resulting in a problematic or bad cosine series fit; thus, providing a more flexible and accurate fit by combining multiple dihedral conformational energies in a single dihedral, a strategy used in the original and modern OPLS force fields [Jorgensen:1996: @Chao:2021].  For example, a carboxylic acid with an alkyl tail has two dihedrals in the same rotation cycle; the C-C-C-O: (O: = oxygen without hydrogen) dihedral is set to zero while the C-C-O-H dihedral is fit [@Jorgensen:1996; @Chao:2021; @Ganesh:2004].  The `MoSDeF-dihedral-fit` [@Crawford:2023b] API fills the missing gap by providing a generalized and easy solution to fitting dihedrals in their commonly used forms and outputting the MM dihedral data points so users can fit other custom dihedral forms.
-
-Commonly used force field dihedrals, such as OPLS, were originally fit when the QM simulations used to fit the dihedrals were computationally prohibitive.  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.  These prior assumptions in the dihedral fits may also lead to problems in reproducibility in modified force fields.  Today, with more advanced hardware and software, QM simulations can be conducted with more complex molecules, allowing for higher quality and customized dihedral fits.  The `MoSDeF-dihedral-fit` software will enable scientists to create a generalized, or molecule-specific dihedral parameters, quickly, accurately and reproducibly.
-
+Some integrated dihedral fitting software currently exists for AMBER[@Horton:2022] or CHARMM-style force fields [@Mayne:2013], and other software will fit the dihedral constants to the final MM and QM energies, which need to be calculated by other means [@Guvench:2008].  However, there is a need a simple, generalized software package that supports multiple potential functions, imports QM and MM files, automatically reads and organizes the QM data, calculates the MM energies, auto-corrects the dihedral fit to account for multiple instances of the dihedral, and automatically removes the unusable cosine power series combinations due to this symmetry.  The `MoSDeF-dihedral-fit` software accomplishes all this and automatically accounts for any of the common combining rules and the 1-4 scaling factors specified via the MoSDeF XML (i.e., force field) files [@Cummings:2021; @Summers:2020; @GMSO:2019; @forcefield-utilities:2022].  By allowing the user to set any other dihedral in the molecule to zero, this software avoids forcing one dihedral fit to correct the inaccurate forces of another dihedral, resulting in a problematic or bad cosine series fit; thus, providing a more flexible and accurate fit by combining multiple dihedral conformational energies in a single dihedral, a strategy used in the original and modern OPLS force fields [Jorgensen:1996: @Chao:2021].  For example, a carboxylic acid with an alkyl tail has two dihedrals in the same rotation cycle; the C-C-C-O: (O: = oxygen without hydrogen) dihedral is set to zero while the C-C-O-H dihedral is fit [@Jorgensen:1996; @Chao:2021; @Ganesh:2004].  The `MoSDeF-dihedral-fit` [@Crawford:2023b] API fills the missing gap by providing a generalized and easy solution to fitting dihedrals in their commonly used forms and outputting the MM dihedral data points so users can fit other custom dihedral forms.
 
 # Acknowledgements