added zeroing a dihedral example and citations.

paper/paper.bib

@@ -112,6 +112,19 @@ @article{Jorgensen:1996
 doi = {10.1021/ja9621760}
 }
 
+# OPLS4 FF
+@article{Chao:2021,
+author = {Lu, Chao and Wu, Chuanjie and Ghoreishi, Delaram and Chen, Wei and Wang, Lingle and Damm, Wolfgang and Ross, Gregory A. and Dahlgren, Markus K. and Russell, Ellery and Von Bargen, Christopher D. and Abel, Robert and Friesner, Richard A. and Harder, Edward D.},
+title = {OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space},
+journal = {Journal of Chemical Theory and Computation},
+volume = {17},
+number = {7},
+pages = {4291-4300},
+year = {2021},
+doi = {10.1021/acs.jctc.1c00302},
+URL = {https://doi.org/10.1021/acs.jctc.1c00302},
+}
+
 # Mie FF
 @article{Mie:1903,
 author = {Mie, G.},
@@ -349,11 +362,24 @@ @inproceedings{Stone:2001
   annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
 }
 
-# vmd-python
+# vmd-python GitHub
 @fidgit{vmd-python:2016,
 author = {Robin Betz},
 title = {VMD-python},
 year = {2016},
 publisher = {Github},
 url = {https://github.com/Eigenstate/vmd-python},
 }
+
+# COOH dihedral with zeroing - Potoff
+@article{Ganesh:2004,
+author = {Kamath, Ganesh and Cao, Feng and Potoff, Jeffrey J.},
+title = {An Improved Force Field for the Prediction of the Vapor−Liquid Equilibria for Carboxylic Acids},
+journal = {The Journal of Physical Chemistry B},
+volume = {108},
+number = {37},
+pages = {14130-14136},
+year = {2004},
+doi = {10.1021/jp048581s},
+URL = {https://doi.org/10.1021/jp048581s},
+}

paper/paper.md

@@ -69,7 +69,7 @@ The `MoSDeF-Dihedral-Fit` [@Crawford:2023b] library lets users quickly calculate
 
 Many different types of Molecular Mechanics (MM) simulation models exist, which are also known as "force fields".  While many of these 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., scaling factors between the 1st and 4th atoms) that were used in the development of the original parameters [@Berthelot:1898; @Good:1970; @Lorentz:1881]. The accuracy of these dihedral parameters for each force field is critical for molecular simulations to obtain 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, and automatically fits the dihedral.  Additionally, the molecular simulation community needs software that fits the dihedral to any force field style and auto-corrects the fit to account for multiple instances of the dihedral and molecular symmetry, since fitting these dihedrals is a high barrier to simulating new chemistry and materials if these parameters do not exist for the chosen force field.  The `MoSDeF-dihedral-fit` software accomplishes all this and automatically accounts for any of the common combining rules, allows the zeroing out any other dihedrals in the molecule (i.e., allowing a better fit and user control by setting the other dihedral energies to zero), and accounts for any 1-4 scaling factors specified via the MoSDeF XML files [@Cummings:2021; @Summers:2020; @GMSO:2019; @forcefield-utilities:2022], which contain the force fields. The `MoSDeF-dihedral-fit` [@Crawford:2023b] API fills the missing gap by providing a generalized and easy solution to fitting dihedrals for any dihedral form that is allowable in the Molecular Simulation Design Framework (MoSDeF) and MoSDeF-GOMC (uses the GPU Optimized Monte Carlo - GOMC MM engine) software [@Crawford:2023a; @Crawford:2022; @Crawford:2023b; @Nejahi:2019; @Nejahi:2021].
+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, and automatically fits the dihedral.  Additionally, the molecular simulation community needs software that fits the dihedral to any force field style and auto-corrects the fit to account for multiple instances of the dihedral and molecular symmetry, since fitting these dihedrals is a high barrier to simulating new chemistry and materials if these parameters do not exist for the chosen force field.  The `MoSDeF-dihedral-fit` software accomplishes all this and automatically accounts for any of the common combining rules, allows the zeroing out any other dihedrals in the molecule (i.e., allowing a better fit and user control by setting the other dihedral energies to zero), and accounts for any 1-4 scaling factors specified via the MoSDeF XML files [@Cummings:2021; @Summers:2020; @GMSO:2019; @forcefield-utilities:2022], which contain the force fields. For example, two dihedrals in the same rotation cycle that both start at the carbon chain and end with a carboxylic acid demonstrate that setting one dihedral to zero is a typical practice, as the C-C-C-O: (O: = oxygen without hydrogen) dihedral is set to zero while the C-C-C-O (O = oxygen with hydrogen) is the only fit or non-zero dihedral [@Jorgensen:1996; @Chao:2021; @Ganesh:2004]. Setting one dihedral to zero avoids potentially incorrect forces and a problematic or bad cosine series dihedral fit; otherwise, it would require fitting the first dihedral with a keytone or alcohol and then fitting the remaining dihedral in the carboxylic acid.  The `MoSDeF-dihedral-fit` [@Crawford:2023b] API fills the missing gap by providing a generalized and easy solution to fitting dihedrals for any dihedral form that is allowable in the Molecular Simulation Design Framework (MoSDeF) and MoSDeF-GOMC (uses the GPU Optimized Monte Carlo - GOMC MM engine) software [@Crawford:2023a; @Crawford:2022; @Crawford:2023b; @Nejahi:2019; @Nejahi:2021].
 
 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 for any force field.
 
@@ -81,14 +81,13 @@ This research was partially supported by the National Science Foundation (grants
 
 Proper dihedral (dihedral) forms.
 
-
 <u>OPLS-dihedral</u>:
 
-$$U_{OPLS} = \frac{f_0}{2}$$
+$$U_{OPLS} = \frac{k_0}{2}$$
 
-$$+ \frac{f_1}{2} * (1 + cos(\theta)) + \frac{f_2}{2} * (1-cos(2 * \theta))$$
+$$+ \frac{k_1}{2} * (1 + cos(\theta)) + \frac{k_2}{2} * (1-cos(2 * \theta))$$
 
-$$+ \frac{f_3}{2} * (1 + cos(3 * \theta)) + \frac{f_4}{2}  *(1-cos(4 * \theta))$$
+$$+ \frac{k_3}{2} * (1 + cos(3 * \theta)) + \frac{k_4}{2}  *(1-cos(4 * \theta))$$
 
 <u>Ryckaert-Bellemans (RB)-torsions</u>: