[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

paper/paper.bib

@@ -82,8 +82,8 @@ @article{Jorgensen:1996
 author = {Jorgensen, W. L. and Maxwell, D. S. and Tirado-Rives, J.},
 title = {Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids},
 journal = {J. Amer. Chem. Soc.},
-year = {1996}, 
-volume = {118(45)}, 
+year = {1996},
+volume = {118(45)},
 pages = {11225--11236},
 }
 
@@ -161,15 +161,15 @@ @article{Lorentz:1881
 pages = {127--136},
 year = {1881}
 }
-# Gaussian software 
+# Gaussian software
 @misc{Gaussian16:2016,
 author={M. J. Frisch and G. W. Trucks and H. B. Schlegel and G. E. Scuseria and M. A. Robb and J. R. Cheeseman and G. Scalmani and V. Barone and G. A. Petersson and H. Nakatsuji and X. Li and M. Caricato and A. V. Marenich and J. Bloino and B. G. Janesko and R. Gomperts and B. Mennucci and H. P. Hratchian and J. V. Ortiz and A. F. Izmaylov and J. L. Sonnenberg and D. Williams-Young and F. Ding and F. Lipparini and F. Egidi and J. Goings and B. Peng and A. Petrone and T. Henderson and D. Ranasinghe and V. G. Zakrzewski and J. Gao and N. Rega and G. Zheng and W. Liang and M. Hada and M. Ehara and K. Toyota and R. Fukuda and J. Hasegawa and M. Ishida and T. Nakajima and Y. Honda and O. Kitao and H. Nakai and T. Vreven and K. Throssell and Montgomery, {Jr.}, J. A. and J. E. Peralta and F. Ogliaro and M. J. Bearpark and J. J. Heyd and E. N. Brothers and K. N. Kudin and V. N. Staroverov and T. A. Keith and R. Kobayashi and J. Normand and K. Raghavachari and A. P. Rendell and J. C. Burant and S. S. Iyengar and J. Tomasi and M. Cossi and J. M. Millam and M. Klene and C. Adamo and R. Cammi and J. W. Ochterski and R. L. Martin and K. Morokuma and O. Farkas and J. B. Foresman and D. J. Fox},
 title={Gaussian 16 {R}evision {C}.01},
 year={2016},
 note={Gaussian Inc. Wallingford CT}
 }
 
-# VMD 
+# VMD
 @article {Humphrey:1996,
 	author = {Humphrey, W. and Dalke, A. and Schulten, K.},
 	title = {(VMD) – (V)isual (M)olecular (D)ynamics},
@@ -184,7 +184,7 @@ @fidgit{GMSO:2019
 author = {},
 title = {GMSO: General Molecular Simulation Object},
 year = {2019},
-publisher = {Github}, 
+publisher = {Github},
 url = {https://github.com/mosdef-hub/gmso},
 }
 

paper/paper.md

@@ -17,21 +17,21 @@ authors:
   - name: Brad Crawford
     orcid: 0000-0003-0638-7333
     equal-contrib: true
-    affiliation: "1, 2" 
+    affiliation: "1, 2"
   - name: Co D. Quach
-    orcid: 
+    orcid:
     affiliation: "3, 4"
   - name: Nicholas C. Craven
-    orcid: 
+    orcid:
     affiliation: "4, 5"
   - name: Christopher R. Iacovella
-    orcid: 
+    orcid:
     affiliation: "3, 4, 5"
   - name: Clare McCabe
     orcid: 0000-0002-8552-9135
     affiliation: "3, 4"
   - name: Peter T. Cummings
-    orcid: 
+    orcid:
     affiliation: "3, 4"
   - name: Jeffrey J. Potoff
     orcid: 0000-0002-4421-8787
@@ -57,16 +57,16 @@ bibliography: paper.bib
 
 # Summary
 
-Molecular Mechanics (MM) simulations (molecular dynamics and Monte Carlo) provide a third method of scientific discovery, simulation modeling, adding to the traditional theoretical and experimental scientific methods.  These molecular simulations provide visual and calculated properties that are difficult, to expensive, or unattainable from the conventional methods.  Additionally, molecular simulations can be utilized to obtain insights and properties on chemicals or materials that do not currently exist, not easily attainable, or require hard-to-achieve state points (i.e., very high pressures and temperatures).  However, these MM models operate from force field parameters determined from Quantum Mechanics (QM) simulations, where the MM proper dihedrals (i.e., dihedrals) are the most difficult to obtain if they don't currently exist for the chosen force field. These MM dihedrals are also not easily transferable between different force fields.  
+Molecular Mechanics (MM) simulations (molecular dynamics and Monte Carlo) provide a third method of scientific discovery, simulation modeling, adding to the traditional theoretical and experimental scientific methods.  These molecular simulations provide visual and calculated properties that are difficult, to expensive, or unattainable from the conventional methods.  Additionally, molecular simulations can be utilized to obtain insights and properties on chemicals or materials that do not currently exist, not easily attainable, or require hard-to-achieve state points (i.e., very high pressures and temperatures).  However, these MM models operate from force field parameters determined from Quantum Mechanics (QM) simulations, where the MM proper dihedrals (i.e., dihedrals) are the most difficult to obtain if they don't currently exist for the chosen force field. These MM dihedrals are also not easily transferable between different force fields.
 
-`MoSDeF-Dihedral-Fit` lets users quickly calculate the MM proper dihedrals (dihedrals) directly from the QM simulations for several force fields (OPLS, CHARMM, TraPPE, AMBER, Mie, and Exp6) [@Jorgensen:1996, @Brooks:2009, @Lee:2016-CG, @Martin:1998, @Weiner:1984, @Weiner:1986, @Mie:1903, @Buckingham:1938].  The user simply has to generate or use an existing Molecular Simulation Design Framework (MoSDeF) force field XML file [@Cummings:2021, @Summers:2020, @GMSO:2019, @forcefield-utilities:2022], provide a Gaussian 16 or Gaussian-style Quantum Mechanics (QM) simulation file that covers the dihedral rotation (typically, 0-360 degrees) and provide the molecular structure information as a mol2 file [@Gaussian16:2016].  This software utilizes the QM and MM data to fit the dihedral to the specific force field, fitting the constants for the OPLS dihedral form.  The `MoSDeF-Dihedral-Fit` software then analytically calculates the Ryckaert-Bellemans (RB)-torsions and the periodic dihedral from the OPLS dihedral fit.  If another dihedral form is needed, the software outputs the raw data points to fit any other dihedral form.  Therefore, the `MoSDeF-Dihedral-Fit` software allows the fitting of any dihedral form, provided the force fields are supported by MoSDeF/MoSDeF-GOMC software, and the QM data is provided as a Gaussian output file or a generalized Gaussian-style output form.  
+`MoSDeF-Dihedral-Fit` lets users quickly calculate the MM proper dihedrals (dihedrals) directly from the QM simulations for several force fields (OPLS, CHARMM, TraPPE, AMBER, Mie, and Exp6) [@Jorgensen:1996, @Brooks:2009, @Lee:2016-CG, @Martin:1998, @Weiner:1984, @Weiner:1986, @Mie:1903, @Buckingham:1938].  The user simply has to generate or use an existing Molecular Simulation Design Framework (MoSDeF) force field XML file [@Cummings:2021, @Summers:2020, @GMSO:2019, @forcefield-utilities:2022], provide a Gaussian 16 or Gaussian-style Quantum Mechanics (QM) simulation file that covers the dihedral rotation (typically, 0-360 degrees) and provide the molecular structure information as a mol2 file [@Gaussian16:2016].  This software utilizes the QM and MM data to fit the dihedral to the specific force field, fitting the constants for the OPLS dihedral form.  The `MoSDeF-Dihedral-Fit` software then analytically calculates the Ryckaert-Bellemans (RB)-torsions and the periodic dihedral from the OPLS dihedral fit.  If another dihedral form is needed, the software outputs the raw data points to fit any other dihedral form.  Therefore, the `MoSDeF-Dihedral-Fit` software allows the fitting of any dihedral form, provided the force fields are supported by MoSDeF/MoSDeF-GOMC software, and the QM data is provided as a Gaussian output file or a generalized Gaussian-style output form.
 
 
 # Statement of need
 
-Many different types of Molecular Mechanics (MM) simulation models exist, also called 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 between force fields due to the different combining rules (arithmetic and geometric) and 1-4 scaling factors (i.e., scaling factors between the 1st and 4th atoms) differing between the force fields [@Berthelot:1898, @Good:1970, @Lorentz:1881].   
+Many different types of Molecular Mechanics (MM) simulation models exist, also called 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 between force fields due to the different combining rules (arithmetic and geometric) and 1-4 scaling factors (i.e., scaling factors between the 1st and 4th atoms) differing between the force fields [@Berthelot:1898, @Good:1970, @Lorentz:1881].
 
-While some dihedral fitting software currently exists, they are not generalized (add NAMDE one here) or only fit the dihedral constants to the final points that need to be calculated by other means (add one here).  Therefore, a generalized software package is desired in the molecular simulation community, as fitting these dihedrals is a high barrier to simulating new chemistry and materials if these parameters do not currently exist for the desired force field.  The `MoSDeF-Dihedral-Fit` software fills the missing gap by providing a generalized and easy solution to fitting dihedrals for a dihedral form that is allowable in the MoSDeF/MoSDeF-GOMC software.  
+While some dihedral fitting software currently exists, they are not generalized (add NAMDE one here) or only fit the dihedral constants to the final points that need to be calculated by other means (add one here).  Therefore, a generalized software package is desired in the molecular simulation community, as fitting these dihedrals is a high barrier to simulating new chemistry and materials if these parameters do not currently exist for the desired force field.  The `MoSDeF-Dihedral-Fit` software fills the missing gap by providing a generalized and easy solution to fitting dihedrals for a dihedral form that is allowable in the MoSDeF/MoSDeF-GOMC software.
 
 
 # Mathematics
@@ -111,6 +111,6 @@ Figure sizes can be customized by adding an optional second parameter:
 
 # Acknowledgements
 
-This research was partially supported by the National Science Foundation (grants OAC-1835713, OAC-1835874, and CBET 2052438).  Atomfold LLC also donated research and development time and computational resources for this research and software.  Wayne State University Grid provided some of the computational resources used in this work. 
+This research was partially supported by the National Science Foundation (grants OAC-1835713, OAC-1835874, and CBET 2052438).  Atomfold LLC also donated research and development time and computational resources for this research and software.  Wayne State University Grid provided some of the computational resources used in this work.
 
-# References
+# References