added References title and fixed one reference for the JOSS paper.

paper/paper.md

@@ -69,7 +69,7 @@ The `MoSDeF-Dihedral-Fit` [@Crawford:2023b] library allows users to quickly calc
 
 While many of these MM force field parameters can be transferred between force fields, such as bonds, angles, and improper dihedrals (often referred to as "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 required for understanding and analyzing the system's microstructure and physical properties (e.g., free energies, viscosities, adsorption loading, diffusion constants, and many more).
 
-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 for 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.
+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 for 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
 
@@ -80,7 +80,7 @@ This research was partially supported by the National Science Foundation (grants
 
 **Proper dihedral (dihedral) forms**
 
-<u>OPLS-dihedral</u>:
+<u>OPLS dihedral</u>:
 
 $$ U_{OPLS} = \frac{k_0}{2} $$
 
@@ -104,7 +104,7 @@ $$+ C_3 * cos(\psi)^3 + C_4 * cos(\psi)^4$$
 \label{eqn:RBeqn}
 \end{equation}
 
-<u>Periodic-dihedral</u>:
+<u>Periodic dihedral</u>:
 
 $$U_{Periodic} = K_0 * (1 + cos(n_0*\theta - d_0))$$
 
@@ -118,3 +118,5 @@ $$where:  n_0 = 0  ;  n_1 = 1  ;  n_2 = 2  ;  n_3 = 3  ;  n_4 = 4 $$
 d_0 = 90^o  ;  d_1 = 180^o  ;  d_2 = 0^o  ;  d_3 = 180^o  ;  d_4 = 0^o
 \label{eqn:periodiceqn}
 \end{equation}
+
+# References