Deleted obsolete documentation files

docs/usersguide/references.bib

-@article{Andersen1980
-   author = {Andersen, Hans C.},
-   title = {Molecular dynamics simulations at constant pressure and/or temperature},
-   journal = {Journal of Chemical Physics},
-   volume = {72},
-   number = {4},
-   pages = {2384-2393},
-   year = {1980},
-   type = {Journal Article}
-}
-
-@article{Aqvist2004
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-   journal = {Chemical Physics Letters},
-   volume = {384},
-   pages = {288-294},
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-   type = {Journal Article}
-}
-
-@article{Berendsen1987
-   author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
-   title = {The missing term in effective pair potentials},
-   journal = {Journal of Physical Chemistry},
-   volume = {91},
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-   type = {Journal Article}
-}
-
-@article{Ceriotti2010
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-   journal = {Journal of Chemical Physics},
-   volume = {133},
-   number = {12},
-   year = {2010},
-   type = {Journal Article}
-}
-
-@article{Chow1995
-   author = {Chow, Kim-Hung and Ferguson, David M.},
-   title = {Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling},
-   journal = {Computer Physics Communications},
-   volume = {91},
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-   type = {Journal Article}
-}
-
-@article{Craig2004
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-   journal = {Journal of Chemical Physics},
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-   type = {Journal Article}
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-
-@article{Duan2003
-   author = {Duan, Y.; Wu, C. and Chowdhury, S. and Lee, M.C. and Xiong, G. and Zhang, W. and Yang, R. and Cieplak, P. and Luo, R. and Lee, T.},
-   title = {A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations},
-   journal = {Journal of Computational Chemistry},
-   volume = {24},
-   pages = {1999-2012},
-   year = {2003},
-   type = {Journal Article}
-}
-
-@article{Essmann1995
-   author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
-   title = {A smooth particle mesh Ewald method},
-   journal = {Journal of Chemical Physics},
-   volume = {103},
-   number = {19},
-   pages = {8577-8593},
-   year = {1995},
-   type = {Journal Article}
-}
-
-@article{Hall1984
-   author = {Hall, Randall W. and Berne, B. J.},
-   title = {Nonergodicity in path integral molecular dynamics},
-   journal = {Journal of Chemical Physics},
-   volume = {81},
-   number = {8},
-   year = {1984},
-   type = {Journal Article}
-}
-
-@article{Hawkins1995
-   author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
-   title = {Pairwise solute descreening of solute charges from a dielectric medium},
-   journal = {Chemical Physics Letters},
-   volume = {246},
-   number = {1-2},
-   pages = {122-129},
-   year = {1995},
-   type = {Journal Article}
-}
-
-@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},
-   title = {Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew},
-   journal = {Journal of Chemical Physics},
-   volume = {120},
-   pages = {9665-9678},
-   year = {2004},
-   type = {Journal Article}
-}
-
-@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},
-   journal = {Proteins},
-   volume = {65},
-   pages = {712-725},
-   year = {2006},
-   type = {Journal Article}
-}
-
-@article{Izaguirre2010
-   author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
-   title = {Multiscale dynamics of macromolecules using Normal Mode Langevin},
-   journal = {Pacific Symposium on Biocomputing},
-   volume = {15},
-   pages = {240-251},
-   year = {2010},
-   type = {Journal Article}
-}
-
-@article{Jorgensen1983
-   author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
-   title = {Comparison of simple potential functions for simulating liquid water},
-   journal = {Journal of Chemical Physics},
-   volume = {79},
-   pages = {926-935},
-   year = {1983},
-   type = {Journal Article}
-}
-
-@inbook{Kollman1997
-   author = {Kollman, P.A. and Dixon, R. and Cornell, W. and Fox, T. and Chipot, C. and Pohorille, A.},
-   title = {Computer Simulation of Biomolecular Systems},
-   editor = {Wilkinson, A. and Weiner, P. and van Gunsteren, Wilfred F.},
-   publisher = {Elsevier},
-   volume = {3},
-   pages = {83-96},
-   year = {1997},
-   type = {Book Section}
-}
-
-@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},
-   journal = {Journal of Computational Chemistry},
-   volume = {29},
-   number = {10},
-   pages = {1693-1698},
-   year = {2008},
-   type = {Journal Article}
-}
-
-@article{Lamoureux2006
-   author = {Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V. and Roux, Benoit and MacKerell Jr., Alexander D.},
-   title = {A polarizable model of water for molecular dynamics simulations of biomolecules},
-   journal = {Chemical Physics Letters},
-   volume = {418},
-   number = {1-3},
-   pages = {245-249},
-   year = {2006},
-   type = {Journal Article}
-}
-
-@article{Lamoureux2003
-   author = {Lamoureux, Guillaume and Roux, Benoit},
-   title = {Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm},
-   journal = {Journal of Chemical Physics},
-   volume = {119},
-   number = {6},
-   pages = {3025-3039},
-   year = {2003},
-   type = {Journal Article}
-}
-
-@article{Li2010
-   author = {Li, D.W. and Br{\"u}schweiler, R.},
-   title = {NMR-based protein potentials},
-   journal = {Angewandte Chemie International Edition},
-   volume = {49},
-   pages = {6778-6780},
-   year = {2010},
-   type = {Journal Article}
-}
-
-@article{Lindorff-Larsen2010
-   author = {Lindorff-Larsen, K. and Piana, S. and Palmo, K. and Maragakis, P. and Klepeis, J. and Dror, R.O. and Shaw, D.E.},
-   title = {Improved side-chain torsion potentials for the Amber ff99SB protein force field},
-   journal = {Proteins},
-   volume = {78},
-   pages = {1950-1958},
-   year = {2010},
-   type = {Journal Article}
-}
-
-@article{Liu1989
-   author = {Liu, Dong C. and Nocedal, Jorge},
-   title = {On the Limited Memory BFGS Method For Large Scale Optimization},
-   journal = {Mathematical Programming},
-   volume = {45},
-   pages = {503-528},
-   year = {1989},
-   type = {Journal Article}
-}
-
-@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},
-    volume = {9},
-    number = {12},
-    pages = {5430-5449},
-    year = {2013},
-    type = {Journal Article}
-}
-
-@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},
-   journal = {Journal of Chemical Physics},
-   volume = {112},
-   pages = {8910-8922},
-   year = {2000},
-   type = {Journal Article}
-}
-
-@article{Markland2008
-   author = {Markland, Thomas E. and Manolopoulos, David E.},
-   title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
-   journal = {Journal of Chemical Physics},
-   volume = {129},
-   number = {2},
-   year = {2008},
-   type = {Journal Article}
-}
-
-@article{Mongan2007
-   author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
-   title = {Generalized Born model with a simple, robust molecular volume correction},
-   journal = {Journal of Chemical Theory and Computation},
-   volume = {3},
-   number = {1},
-   pages = {156-169},
-   year = {2007},
-   type = {Journal Article}
-}
-
-@article{Nguyen2013
-   author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
-   title = {Improved Generalized Born Solvent Model Parameters for Protein Simulations},
-   journal = {Journal of Chemical Theory and Computation},
-   volume = {9},
-   number = {4},
-   pages = {2020-2034},
-   year = {2013},
-   type = {Journal Article}
-}
-
-@article{Onufriev2004
-   author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
-   title = {Exploring protein native states and large-scale conformational changes with a modified generalized born model},
-   journal = {Proteins},
-   volume = {55},
-   number = {22},
-   pages = {383-394},
-   year = {2004},
-   type = {Journal Article}
-}
-
-@article{Parrinello1984
-   author = {Parrinello, M. and Rahman, A.},
-   title = {Study of an F center in molten KCl},
-   journal = {Journal of Chemical Physics},
-   volume = {80},
-   number = {2},
-   pages = {860-867},
-   year = {1984},
-   type = {Journal Article}
-}
-
-@misc{Ponder
-   author = {Ponder, Jay W.},
-   title = {Personal communication},
-   type = {Personal Communication}
-}
-
-@article{Ren2002
-   author = {Ren, P. and Ponder, Jay W.},
-   title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
-   journal = {Journal of Computational Chemistry},
-   volume = {23},
-   pages = {1497-1506},
-   year = {2002},
-   type = {Journal Article}
-}
-
-@article{Ren2003
-   author = {Ren, P. and Ponder, Jay W.},
-   title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
-   journal = {Journal of Physical Chemistry B},
-   volume = {107},
-   pages = {5933-5947},
-   year = {2003},
-   type = {Journal Article}
-}
-
-@article{Schaefer1998
-   author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
-   title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
-   journal = {Journal of Molecular Biology},
-   volume = {284},
-   number = {3},
-   pages = {835-848},
-   year = {1998},
-   type = {Journal Article}
-}
-
-@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},
-   volume = {3},
-   pages = {2083-2097},
-   year = {2007},
-   type = {Journal Article}
-}
-
-@article{Shirts2008
-   author = {Shirts, Michael R. and Chodera, John D.},
-   title = {Statistically optimal analysis of samples from multiple equilibrium states},
-   journal = {Journal of Chemical Physics},
-   volume = {129},
-   pages = {124105},
-   year = {2008},
-   type = {Journal Article}
-}
-
-@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},
-   pages = {4046-4063},
-   year = {2013},
-   type = {Journal Article}
-}
-
-@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},
-   journal = {Journal of Physical Chemistry B},
-   volume = {111},
-   pages = {13052-13063},
-   year = {2007},
-   type = {Journal Article}
-}
-
-@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},
-   journal = {Journal of Chemical Physics},
-   volume = {132},
-   pages = {134508},
-   year = {2005},
-   type = {Journal Article}
-}
-
-@article{Thole1981
-   author = {Thole, B. T.},
-   title = {Molecular polarizabilities calculated with a modified dipole interaction},
-   journal = {Chemical Physics},
-   volume = {59},
-   number = {3},
-   pages = {341-350},
-   year = {1981},
-   type = {Journal Article}
-}
-
-@article{Tironi1995
-   author = {Tironi, Ilario G. and Sperb, René and Smith, Paul E. and van Gunsteren, Wilfred F.},
-   title = {A generalized reaction field method for molecular dynamics simulations},
-   journal = {Journal of Chemical Physics},
-   volume = {102},
-   number = {13},
-   pages = {5451-5459},
-   year = {1995},
-   type = {Journal Article}
-}
-
-@article{Toukmaji1996
-   author = {Toukmaji, Abdulnour Y.  and Board Jr, John A.},
-   title = {Ewald summation techniques in perspective: a survey},
-   journal = {Computer Physics Communications},
-   volume = {95},
-   pages = {73-92},
-   year = {1996},
-   type = {Journal Article}
-}
-
-@article{Wang2000
-   author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
-   title = {How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?},
-   journal = {Journal of Computational Chemistry},
-   volume = {21},
-   pages = {1049-1074},
-   year = {2000},
-   type = {Journal Article}
-}
-
-@article{Wang2014
-   author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
-   title = {Building force fields: an automatic, systematic, and reproducible approach},
-   journal = {Journal of Physical Chemistry Letters},
-   volume = {5},
-   pages = {1885-1891},
-   year = {2014},
-   type = {Journal Article}
-}

docs/usersguide/zbibliography.rst

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