initial JOSS paper commit

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}
+}