diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 0000000..e644263 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,302 @@ +# FF fitting VMD force field toolkit (fftk) +@article{Mayne:2013, +author = {Mayne, C.G. Mayne and Saam, J, and Schulten, K. and Tajkhorshid, E. and Gumbart, J.C.}, +journal = {J. Comp. Chem.}, +volume = {34}, +issue = {32} +pages = {2757-2770}, +title = {{Rapid parameterization of small molecules using the force field toolkit}}, +doi = {10.1002/jcc.23422}, +url = {https://doi.org/10.1002/jcc.23422}, +year = {2013} +} + +# FF fitting MacKerell/Guvench +@article{Guvench:2008, +author = {Guvench, O. and MacKerell, A.D.}, +journal = {J. Mol. Model.}, +volume = {14}, +pages = {667-679}, +title = {{Automated conformational energy fitting for force-field development}}, +doi = {10.1007/s00894-008-0305-0}, +url = {https://doi.org/10.1007/s00894-008-0305-0}, +year = {1998} +} + +# Trappe FF +@article{Martin:1998, +author = {Martin, Marcus G and Siepmann, J Ilja}, +doi = {10.1021/jp972543+}, +issn = {15206106}, +journal = {J. Phys. Chem. B}, +number = {14}, +pages = {2569--2577}, +title = {{Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes}}, +url = {https://pubs.acs.org/sharingguidelines}, +volume = {102}, +year = {1998} +} + +# EXP6 part 1 +@article{Buckingham:1938, +author = {Buckingham, R.A.}, +title = {The classical equation of state of gaseous helium, neon and argon}, +journal = {Proceedings of the royal society A}, +volume = {168}, +issue = {933}, +year = {1939}, +doi = {10.1098/rspa.1938.0173}, +URL = {https://doi.org/10.1098/rspa.1938.0173}, +} + +# EXP6 part 2 +@article{Mason:1954, +author = {Mason, E.A.}, +title = {Transport Properties of Gases Obeying a Modified Buckingham (Exp‐Six) Potential }, +journal = {The Journal of Chemical Physics}, +volume = {22}, +issue = {2}, +pages = {169-186}, +year = {1954}, +doi = {10.1063/1.1740026}, +URL = {https://doi.org/10.1063/1.1740026}, +} + +# AMBER part 1 +@article{Weiner:1984, +author = {Weiner, Scott J. and Kollman, Peter A. and Case, David A. and Singh, U. Chandra and Ghio, Caterina and Alagona, Guliano and Profeta, Salvatore and Weiner, Paul}, +title = {A new force field for molecular mechanical simulation of nucleic acids and proteins}, +journal = {Journal of the American Chemical Society}, +volume = {106}, +number = {3}, +pages = {765-784}, +year = {1984}, +doi = {10.1021/ja00315a051}, +URL = {https://doi.org/10.1021/ja00315a051}, +} + +# AMBER part 2 +@article{Weiner:1986, +author = {Weiner, S.J. and Kollman, P.A. and Nguyen D.T. Nguyen and Case, D.A.}, +title = {An all atom force field for simulations of proteins and nucleic acids}, +journal = {J. Comp. Chem.}, +volume = {7}, +issue = {2}, +pages = {230-252}, +year = {986}, +doi = {10.1002/jcc.540070216}, + +URL = {https://doi.org/10.1002/jcc.540070216}, +} + +# AMBER GAFF FF +@article{Wang:2004, +author = {Wang, J. and Wolf, R.M. Wolf and J.W. Caldwell, J.W. and Kollman, P.A. and Case, D.A.}, +title = {Development and testing of a general amber force field}, +journal = {J. Comp. Chem.}, +volume = {25}, +issue = {9}, +pages = {1157-1174}, +year = {2004}, +doi = {10.1002/jcc.20035}, +URL = {https://doi.org/10.1002/jcc.20035}, +} + +# OPLS FF +@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)}, +pages = {11225--11236}, +} + +# Mie FF +@article{Mie:1903, +author = {Mie, G.}, +title = {}, +journal = {Ann. Phys.}, +year = {1903}, +volume = {11}, +pages = {657} +} + +# CHARMM FF part 1 +@article{Brooks:2009, +author = {Brooks, B. R. and Brooks, C. L. and Mackerell, A. D. and Nilsson, L. and Petrella, R. J. and Roux, B. and Won, Y. and Archontis, G. and Bartels, C. and Boresch, S. and Caflisch, A. and Caves, L. and Cui, Q. and Dinner, A. R. and Feig, M. and Fischer, S. and Gao, J. and Hodoscek, M. and Im, W. and Kuczera, K. and Lazaridis, T. and Ma, J. and Ovchinnikov, V. and Paci, E. and Pastor, R. W. and Post, C. B. and Pu, J. Z. and Schaefer, M. and Tidor, B. and Venable, R. M. and Woodcock, H. L. and Wu, X. and Yang, W. and York, D. M. and Karplus, M.}, +doi = {10.1002/jcc.21287}, +issn = {1096987X}, +journal = {J.~Comput.\ Chem.}, +keywords = {Biomolecular simulation,Biophysical computation,CHARMM program,Energy function,Molecular dynamics,Molecular mechanics,Molecular modeling}, +month = {jul}, +number = {10}, +pages = {1545--1614}, +pmid = {19444816}, +publisher = {John Wiley and Sons Inc.}, +title = {{CHARMM: The biomolecular simulation program}}, +volume = {30}, +year = {2009} +} + +# CHARMM FF part 2 +@article{Lee:2016-CG, +author = {Lee, Jumin and Cheng, Xi and Swails, Jason M. and Yeom, Min Sun and Eastman, Peter K. and Lemkul, Justin A. and Wei, Shuai and Buckner, Joshua and Jeong, Jong Cheol and Qi, Yifei and Jo, Sunhwan and Pande, Vijay S. and Case, David A. and Brooks, Charles L. and MacKerell, Alexander D. and Klauda, Jeffery B. and Im, Wonpil}, +doi = {10.1021/acs.jctc.5b00935}, +issn = {15499626}, +journal = {J. Chem. Theor. Comput.}, +month = {jan}, +number = {1}, +pages = {405--413}, +pmid = {26631602}, +publisher = {American Chemical Society}, +title = {{CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field}}, +url = {https://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00935}, +volume = {12}, +year = {2016} +} + +# Mixing rule geometric and arithmetic epslion +@article{Berthelot:1898, +author = {Daniel Berthelot}, +title = {Sur le m\'elange des gaz}, +journal = {Comptes Rendus Hebd.~Acad.~Sci.}, +year = {1898}, +volume = {126}, +pages = {1703--1855} +} + +# Mixing rule arithmetic epslion +@article{Good:1970, +author = {Good, Robert J. and Hope, Christopher J.}, +title = {New Combining Rule for Intermolecular Distances in Intermolecular Potential Functions}, +journal = {J.~Chem.\ Phys.}, +volume = {53}, +pages = {540--543}, +DOI = {10.1063/1.1674022}, +year = {1970} +} + +# Mixing rule arithmetic sigma +@article{Lorentz:1881, +author = {Lorentz, H. A.}, +title = {Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase}, +journal = {Ann. d. Phys.}, +volume = {12}, +pages = {127--136}, +year = {1881} +} + +# 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} +} + +# MoSDeF GMSO +@fidgit{GMSO:2019, +author = {}, +title = {GMSO: General Molecular Simulation Object}, +year = {2019}, +publisher = {Github}, +url = {https://github.com/mosdef-hub/gmso}, +} + +# MoSDeF forcefield-utilities +@fidgit{forcefield-utilities:2022, +author = {}, +title = {forcefield-utilities}, +year = {2022}, +publisher = "Github", +url = {https://github.com/mosdef-hub/forcefield-utilities}, +} + +# MoSDeF part 1 +@article{Cummings:2021, +author = {Cummings, P.T. and McCabe, C. and Iacovella, C.R. and Ledeczi, A. and Jankowski, E. and Jayaraman, A. and Palmer, J.C. and Maginn, E.J. and Glotzer, S.C. and Anderson, J.A. and Siepmann, J.I. and Potoff, J. and Matsumoto, R.A. and Gilmer, J.B. and DeFever, R.S. and Singh, R. and Crawford, B.}, +Title = {Open-Source Molecular Modeling Software in Chemical Engineering, with Focus on the Molecular Simulation Design Framework (MoSDeF)}, +journal = {AICHE J.}, +volume = {67(3)}, +pages = {e17206}, +year = {2021} +} + +# MoSDeF part 2 +@article{Summers:2020, +author = {Summers, Andrew Z. and Gilmer, Justin B. and Iacovella, Christopher R. and Cummings, Peter T. and Mccabe, Clare}, +doi = {10.1021/acs.jctc.9b01183}, +issn = {15499626}, +journal = {J. Chem. Theor. Comput.}, +month = {mar}, +number = {3}, +pages = {1779--1793}, +pmid = {32004433}, +publisher = {American Chemical Society}, +title = {{MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films}}, +url = {https://pubs.acs.org/doi/full/10.1021/acs.jctc.9b01183}, +volume = {16}, +year = {2020} +} + +# MoSDeF-dihedral-fit GitHub +@fidgit{Crawford:2023b, + author = "Crawford, Brad and Quach, Co and Craven, Nicholas and Iacovella, Christopher R. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey", + title = "MoSDeF-dihedral-fit: A simple software package to fit dihedrals via the MoSDeF software.", + year = "2023", + publisher = "Github", + url = "https://github.com/GOMC-WSU/MoSDeF-dihedral-fit" +} + +# MoSDeF-GOMC part 1 +@article{Crawford:2023a, +author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.}, +title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC}, +journal = {Journal of Chemical Information and Modeling}, +volume = {63}, +number = {4}, +pages = {1218-1228}, +year = {2023}, +doi = {10.1021/acs.jcim.2c01498}, + note ={PMID: 36791286}, +URL = {https://doi.org/10.1021/acs.jcim.2c01498}, +} + +# MoSDeF-GOMC part 2 +@fidgit{Crawford:2022, + author = "Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas and Gilmer, Justin and Cummings, Peter T. and Potoff, Jeffrey", + title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC", + year = "2022", + publisher = "Github", + url = "https://github.com/GOMC-WSU/MoSDeF-GOMC" +} + +# GOMC part 1 +@article{Nejahi:2019, +author = {Nejahi, Younes and {Soroush Barhaghi}, Mohammad and Mick, Jason and Jackman, Brock and Rushaidat, Kamel and Li, Yuanzhe and Schwiebert, Loren and Potoff, Jeffrey}, +doi = {10.1016/j.softx.2018.11.005}, +issn = {23527110}, +journal = {SoftwareX}, +keywords = {Adsorption,GPU,Gibbs ensemble,Molecular simulation,Monte Carlo,Phase equilibrium}, +pages = {20--27}, +publisher = {Elsevier B.V.}, +title = {{GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids}}, +url = {https://doi.org/10.1016/j.softx.2018.11.005}, +volume = {9}, +year = {2019} +} + +# GOMC part 2 +@article{Nejahi:2021, +author = {Nejahi, Younes and Soroush Barhaghi, Mohammad and Schwing, Gregory and Schwiebert, Loren and Potoff, Jeffrey}, +doi = {10.1016/j.softx.2020.100627}, +issn = {23527110}, +journal = {SoftwareX}, +keywords = {Alchemical free energy,Crankshaft move,Cyclic molecules,Exp-6 potential,Molecular Exchange Monte Carlo,Multi-particle}, +pages = {100627}, +publisher = {Elsevier B.V.}, +title = {{Update 2.70 to “GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids”}}, +volume = {13}, +year = {2021} +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 0000000..f12abc4 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,103 @@ + +--- +title: 'MoSDeF-dihedral-fit: A simple software package to fit dihedrals via the MoSDeF software' + +tags: + - Python + - Molecular simulations + - Molecular mechanics + - Molecular dynamics + - Monte Carlo + - Quantum mechanics + - dihedral fitting + - torsion fitting + - force field + - MoSDeF + - GOMC + - MoSDeF-GOMC + +authors: + - name: Brad Crawford + orcid: 0000-0003-0638-7333 + equal-contrib: true + affiliation: "1, 2" + - name: Co D. Quach + orcid: 0000-0002-1255-4161 + affiliation: "3, 4" + - name: Nicholas C. Craven + orcid: 0000-0002-4607-4377 + affiliation: "4, 5" + - name: Christopher R. Iacovella + orcid: + affiliation: "3, 4, 5" + - name: Clare McCabe + orcid: 0000-0002-8552-9135 + affiliation: "3, 4" + - name: Peter T. Cummings + orcid: 0000-0002-9766-2216 + affiliation: "3, 4" + - name: Jeffrey J. Potoff + orcid: 0000-0002-4421-8787 + equal-contrib: true + affiliation: 2 + +affiliations: + - name: Atomfold LLC, PA, USA + index: 1 + - name: Department of Chemical Engineering, Wayne State University, Detroit, MI 48202-4050, USA + index: 2 + - name: Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, USA + index: 3 + - name: Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37212, USA + index: 4 + - name: Interdisciplinary Material Science Program, Vanderbilt University, Nashville, TN 37235-0106, USA + index: 5 + +date: 31 December 2023 +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 visualizations and calculated properties that are difficult, too expensive, or unattainable by the conventional methods. Additionally, molecular simulations can be utilized to obtain insights and properties on chemicals or materials that do not currently exist, are not easily attainable, or require hard-to-achieve conditions (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. + +The `MoSDeF-Dihedral-Fit` [@Crawford:2023b] library 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 files that covers the dihedral rotation (typically, 0-360 degrees) and provide the molecular structure information in a mol2 format [@Gaussian16:2016]. The `MoSDeF-Dihedral-Fit` software utilizes the QM and MM data to fit the dihedral to the specific force field, fitting the constants for the OPLS dihedral equation form with the correct combining rules and 1-4 scaling factors, as specified in the MoSDeF XML force field file. The `MoSDeF-Dihedral-Fit` software then analytically calculates the Ryckaert-Bellemans (RB)-torsions and the periodic dihedral from the OPLS dihedral. If another dihedral equation 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 and MoSDeF-GOMC (uses the GPU Optimized Monte Carlo - GOMC MM engine) software [Crawford:2023a; Crawford:2022; @Crawford:2023b; Nejahi:2019; Nejahi:2021], and the QM data is provided as a Gaussian output file or a generalized Gaussian-style output form [Gaussian16:2016]. + + +# 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]. + +While some dihedral fitting software currently exists, they are not generalized and only fit the CHARMM-style force fields [@Mayne:2013], or only fit the dihedral constants to the final MM and QM energies that need to be calculated by other means [@Guvench:2008]. Therefore, the molecular simulation community needs a generalized software package that imports the QM and MM files, automatically reads and organizes the QM data, and calculates the MM energies. Additionally, the molecular simulation community needs software that fits the dihedral to any force field style 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 automatically accounts and fits the dihedral for any common combining rules and any 1-4 scaling factors used 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]. + +# 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. + +# Mathematics + +Proper dihedral (dihedral) forms. + + +OPLS-dihedral: + +$$OPLS_{Energy} = \frac{f_0}{2}$$ + +$$+ \frac{f_1}{2}*(1+cos(\theta)) + \frac{f_2}{2}*(1-cos(2*\theta))$$ +$$+ \frac{f_3}{2}*(1+cos(3*\theta)) + \frac{f_4}{2}*(1-cos(4*\theta))$$ + +Ryckaert-Bellemans (RB)-torsions: + +$$RB_{Energy} = C_0$$ +$$+ C_1*cos(\psi) + C_2*cos(\psi)^2$$ +$$+ C_3*cos(\psi)^3 + C_4*cos(\psi)^4$$ +$$ $$ + +$$\psi = \theta - 180^o$$ + +Periodic-dihedral: + +$$Periodic_{Energy} = K_0 * (1 + cos(n_0*\theta - 90^o))$$ +$$+ K_1 * (1 + cos(n_1*\theta - 180^o)) + K_2 * (1 + cos(n_2*\theta))$$ +$$+ K_3 * (1 + cos(n_3*\theta - 180^o)) + K_4 * (1 + cos(n_4*\theta))$$