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@article{Azimi2022,
   author = {Azimi, Solmaz and Khuttan, Sheenam and Wu, Joe Z. and Pal, Rajat K. and Gallicchio, Emilio},
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@article{Barducci2008,
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@article{Basconi2013,
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  doi= {10.1021/ct400109a}
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}

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@article{Berendsen1987
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@article{Best2012,
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   title = {Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone $\phi$, $\psi$, and Side-Chain $\chi$1 and $\chi$2 Dihedral Angles},
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@article{Espanol1995
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@article{Essmann1995
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@article{Everaers2003
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@article{Hall1984
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@article{Hamelberg2007,
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@article{Hawkins1995
   author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
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@article{Horn2004
   author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
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@article{Hornak2006
   author = {Hornak, V. and Abel, R. and Okur, A. and Strockbine, B. and Roitberg, A. and Simmerling, C.},
   title = {Comparison of multiple {Amber} force fields and development of improved protein backbone parameters},
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   pages = {712-725},
   year = {2006},
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@article{Izaguirre2010
   author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
   title = {Multiscale dynamics of macromolecules using {Normal Mode Langevin}},
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}

@article{Jorgensen1983
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@article{Kirschner2007
   author = {Kirschner, Karl N. and Yongye, Austin B. and Tschampel, Sarah M. and González-Outeiriño, Jorge and Daniels, Charlisa R and Foley, B. Lachele and Woods, Robert J.},
   title = {GLYCAM06: A generalizable biomolecular force field. Carbohydrates},
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}

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@inbook{Kollman1997
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@article{Labute2008
   author = {Labute, Paul},
   title = {The generalized {Born}/volume integral implicit solvent model: Estimation of the free energy of hydration using {London} dispersion instead of atomic surface area},
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@article{Lamoureux2006
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@article{Lamoureux2003
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@article{Li2010
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   title = {{NMR}-based protein potentials},
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   title = {Improved side-chain torsion potentials for the {Amber ff99SB} protein force field},
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@article{Lopes2013,
    author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoît and MacKerell, Alexander D.},
    title = {Polarizable Force Field for Peptides and Proteins Based on the Classical {Drude} Oscillator},
    journal = {Journal of Chemical Theory and Computation},
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    number = {12},
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}

@article{Mahoney2000
   author = {Mahoney, Michael W. and Jorgensen, William L.},
   title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
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@article{Maier2015
   author = {Maier, James A. and Martinez, Carmenza and Kasavajhala, Koushik and Wickstrom, Lauren and Hauser, Kevin E. and Simmerling, Carlos},
   title = {ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB},
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   year = {2015},
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@article{Marinari1992,
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@article{Markland2008
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@article{Mongan2007
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@article{Nguyen2013
   author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
   title = {Improved Generalized {Born} Solvent Model Parameters for Protein Simulations},
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   volume = {9},
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   pages = {2020-2034},
   year = {2013},
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@misc{Ponder
   author = {Ponder, Jay W.},
   title = {Personal communication},
   type = {Personal Communication}
}

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@article{Price2004
   author = {Price, D.J. and Brooks, C.L. III},
   title = {A modified TIP3P water potential for simulation with Ewald summation},
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   year = {2004},
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@article{Ren2002
   author = {Ren, P. and Ponder, Jay W.},
   title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
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   year = {2002},
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}

@article{Ren2003
   author = {Ren, P. and Ponder, Jay W.},
   title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
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   year = {2003},
   type = {Journal Article}
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@article{Rick2004
   author = {Rick, S.W.},
   title = {A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums},
   journal = {Journal of Chemical Physics},
   volume = {120},
   pages = {6085-6093},
   year = {2004},
   type = {Journal Article}
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@article{Schaefer1998
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@article{Schnieders2007
   author = {Schnieders, Michael J. and Ponder, Jay W.},
   title = {Polarizable Atomic Multipole Solutes in a Generalized {Kirkwood} Continuum},
   journal = {Journal of Chemical Theory and Computation},
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@article{Shirts2008
   author = {Shirts, Michael R. and Chodera, John D.},
   title = {Statistically optimal analysis of samples from multiple equilibrium states},
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@article{Shi2013
   author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
   title = {Polarizable Atomic Multipole-Based {AMOEBA} Force Field for Proteins},
   journal = {Journal of Chemical Theory and Computation},
   volume = {9},
   number = {9},
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   year = {2013},
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}

@article{Shirts2007
   author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
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}

@article{Shirts2005
   author = {Shirts, Michael R. and Pande, Vijay S.},
   title = {Solvation free energies of amino acid side chain analogs for common molecular mechanics water models},
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}

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@article{Simmonett2015
   author = {Simmonett, Andrew C. and Pickard, Frank C. and Shao, Yihan and Cheatham, Thomas E. and Brooks, Bernard R.},
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@article{Sindhikara2009,
  author =   {Sindhikara, Daniel J. and Kim, Seonah and Voter,
                  Arthur F. and Roitberg, Adrian E.},
  title =    {{Bad Seeds Sprout Perilous Dynamics: Stochastic
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