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gmx-tutorials-refs.bib
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author = "{\v S}ali, Andrej and Blundell, Tom L.",
Date-Added = "2018-08-27 23:58:19 +0000",
Date-Modified = "2018-08-28 00:05:00 +0000",
Journal = "Journal of Molecular Biology",
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Pages = "779--815",
Title = "Comparative Protein Modelling by Satisfaction of Spatial Restraints",
Volume = "234",
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Author = "Braun, Efrem and Gilmer, Justin and Mayes, Heather B. and Mobley, David L. and Monroe, Jacob I. and Prasad, Samarjeet and Zuckerman, Daniel M.",
Date-Added = "2018-08-27 17:18:48 +0000",
Date-Modified = "2018-08-27 17:20:46 +0000",
Journal = "Living Journal of Computational Molecular Science",
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Title = "Best Practices for Foundations in Molecular Simulations [Article v1.0]",
Volume = "1",
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}
@book{Kukol2008,
Editor = "Kukol, Andreas",
Date-Added = "2018-08-27 17:15:25 +0000",
Date-Modified = "2018-08-27 17:16:12 +0000",
Publisher = "Humana Press",
Series = "Methods in Molecular Biology",
Title = "Molecular Modeling of Proteins",
Volume = "443",
Year = "2008"
}
@book{Leach2001,
Author = "Leach, Andrew",
Date-Added = "2018-06-30 23:20:15 +0000",
Date-Modified = "2018-06-30 23:20:41 +0000",
Edition = "2nd",
Publisher = "Pearson",
Title = "Molecular Modelling: Principles and Applications",
Year = "2001"
}
@book{Frenkel2001,
Author = "Frenkel, Daan and Smit, Berend",
Date-Added = "2018-06-30 23:18:48 +0000",
Date-Modified = "2018-06-30 23:21:03 +0000",
Edition = "2nd",
Publisher = "Academic Press",
Series = "Computational Science Series, Vol. 1",
Title = "Understanding Molecular Simulation: From Algorithms to Applications",
Year = "2001"
}
@article{Shirts2008,
author = "Shirts, Michael R. and Chodera, John D.",
Date-Added = "2018-06-26 15:30:15 +0000",
Date-Modified = "2018-06-26 15:30:48 +0000",
Journal = "The Journal of Chemical Physics",
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Title = "Statistically optimal analysis of samples from multiple equilibrium states",
Volume = "129",
Year = "2008",
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issn = "0021-9606"
}
@article{Jo2012,
author = "Jo, Sunhwan and Jiang, Wei and Lee, Hui Sun and Roux, Beno\^it and Im, Wonpil",
Date-Added = "2018-06-26 15:16:41 +0000",
Date-Modified = "2018-06-26 15:17:17 +0000",
Journal = "Journal of Chemical Information and Modeling",
Number = "1",
Pages = "267--277",
Title = "CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application",
Volume = "53",
Year = "2013",
url = "http://dx.doi.org/10.1021/ci300505n",
doi = "10.1021/ci300505n",
issn = "1549-9596"
}
@article{Shirts2005,
author = "Shirts, Michael R. and Pande, Vijay S.",
Date-Added = "2018-06-26 01:27:32 +0000",
Date-Modified = "2018-06-26 01:28:44 +0000",
Journal = "The Journal of Chemical Physics",
Number = "13",
Pages = "134508",
Title = "Solvation free energies of amino acid side chain analogs for common molecular mechanics water models",
Volume = "122",
Year = "2005",
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issn = "0021-9606"
}
@article{Steinbrecher2007,
author = "Steinbrecher, Thomas and Mobley, David L. and Case, David A.",
Date-Added = "2018-06-26 01:24:49 +0000",
Date-Modified = "2018-06-26 01:25:38 +0000",
Journal = "The Journal of Chemical Physics",
Number = "21",
Pages = "214108",
Title = "Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations",
Volume = "127",
Year = "2007",
url = "http://dx.doi.org/10.1063/1.2799191",
doi = "10.1063/1.2799191",
issn = "0021-9606"
}
@article{Pitera2002,
author = "Pitera, Jed W. and van Gunsteren, Wilfred F.",
Date-Added = "2018-06-26 01:23:14 +0000",
Date-Modified = "2018-06-26 01:23:53 +0000",
Journal = "Molecular Simulation",
Number = "1-2",
Pages = "45--65",
Title = "A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations",
Volume = "28",
Year = "2002",
url = "http://dx.doi.org/10.1080/08927020211973",
doi = "10.1080/08927020211973",
issn = "0892-7022"
}
@article{Geyer1995,
author = "Geyer, Charles J. and Thompson, Elizabeth A.",
Date-Added = "2018-06-25 14:14:37 +0000",
Date-Modified = "2018-06-25 14:15:20 +0000",
Journal = "Journal of the American Statistical Association",
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Pages = "909",
Title = "Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference",
Volume = "90",
Year = "1995",
url = "http://dx.doi.org/10.2307/2291325",
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issn = "0162-1459"
}
@article{Marinari1992,
author = "Marinari, E and Parisi, G",
Date-Added = "2018-06-25 14:13:22 +0000",
Date-Modified = "2018-06-25 14:14:17 +0000",
Journal = "Europhysics Letters (EPL)",
Number = "6",
Pages = "451--458",
Title = "Simulated Tempering: A New Monte Carlo Scheme",
Volume = "19",
Year = "1992",
url = "http://dx.doi.org/10.1209/0295-5075/19/6/002",
doi = "10.1209/0295-5075/19/6/002",
issn = "0295-5075"
}
@article{Beutler1994,
author = "Beutler, Thomas C. and Mark, Alan E. and van Schaik, René C. and Gerber, Paul R. and van Gunsteren, Wilfred F.",
Date-Added = "2018-06-25 12:57:56 +0000",
Date-Modified = "2018-06-25 12:59:40 +0000",
Journal = "Chemical Physics Letters",
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Title = "Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations",
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issn = "0009-2614"
}
@article{Shirts2003,
author = "Shirts, Michael R. and Pitera, Jed W. and Swope, William C. and Pande, Vijay S.",
Date-Added = "2018-06-24 18:43:01 +0000",
Date-Modified = "2018-06-24 18:43:53 +0000",
Journal = "The Journal of Chemical Physics",
Number = "11",
Pages = "5740--5761",
Title = "Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins",
Volume = "119",
Year = "2003",
url = "http://dx.doi.org/10.1063/1.1587119",
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issn = "0021-9606"
}
@article{Bennett1976,
author = "Bennett, Charles H",
Date-Added = "2018-06-24 18:31:44 +0000",
Date-Modified = "2018-06-24 18:32:18 +0000",
Journal = "Journal of Computational Physics",
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}
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Author = "Zwanzig, Robert W.",
Date-Added = "2018-06-24 16:49:13 +0000",
Date-Modified = "2018-06-24 16:49:59 +0000",
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Title = "High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases",
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author = "Hanwell, Marcus D and Curtis, Donald E and Lonie, David C and Vandermeersch, Tim and Zurek, Eva and Hutchison, Geoffrey R",
Date-Added = "2018-06-21 22:12:24 +0000",
Date-Modified = "2018-06-21 22:13:18 +0000",
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}
@article{Vanommeslaeghe2012b,
author = "Vanommeslaeghe, K. and Raman, E. Prabhu and MacKerell, Jr., A. D.",
Date-Added = "2018-06-21 22:08:26 +0000",
Date-Modified = "2018-06-21 22:09:14 +0000",
Journal = "Journal of Chemical Information and Modeling",
Number = "12",
Pages = "3155--3168",
Title = "Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges",
Volume = "52",
Year = "2012",
url = "http://dx.doi.org/10.1021/ci3003649",
doi = "10.1021/ci3003649",
issn = "1549-9596"
}
@article{Vanommeslaeghe2012a,
author = "Vanommeslaeghe, K. and MacKerell, Jr., A. D.",
Date-Added = "2018-06-21 22:07:34 +0000",
Date-Modified = "2018-06-21 22:08:25 +0000",
Journal = "Journal of Chemical Information and Modeling",
Number = "12",
Pages = "3144--3154",
Title = "Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing",
Volume = "52",
Year = "2012",
url = "http://dx.doi.org/10.1021/ci300363c",
doi = "10.1021/ci300363c",
issn = "1549-9596"
}
@article{Wang2004,
author = "Wang, Junmei and Wolf, Romain M. and Caldwell, James W. and Kollman, Peter A. and Case, David A.",
Date-Added = "2018-06-20 15:33:50 +0000",
Date-Modified = "2018-06-20 15:34:54 +0000",
Journal = "Journal of Computational Chemistry",
Number = "9",
Pages = "1157--1174",
Title = "Development and testing of a general amber force field",
Volume = "25",
Year = "2004",
url = "http://dx.doi.org/10.1002/jcc.20035",
doi = "10.1002/jcc.20035",
issn = "0192-8651"
}
@article{Vanommeslaeghe2010,
Author = "Vanommeslaeghe, Kenno and Hatcher, E. and Acharya, C. and Kundu, S. and Zhong, S. and Shim, J. and Darian, E. and Guvench, O. and Lopes, P. and Vorobyov, I. and MacKerell, Jr., Alexander D.",
Date-Added = "2018-06-20 15:30:30 +0000",
Date-Modified = "2018-06-20 15:31:46 +0000",
Journal = "Journal of Computational Chemistry",
Number = "4",
Pages = "671-690",
Title = "CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields",
Volume = "31",
Year = "2010",
url = "http://dx.doi.org/10.1002/jcc.21367",
doi = "10.1002/jcc.21367",
issn = "0192-8651"
}
@article{Yang2006,
author = "Yang, Qingyuan and Zhong, Chongli",
Date-Added = "2018-06-19 23:43:48 +0000",
Date-Modified = "2018-06-19 23:44:39 +0000",
Journal = "The Journal of Physical Chemistry B",
Number = "36",
Pages = "17776--17783",
Title = "Molecular Simulation of Carbon Dioxide/Methane/Hydrogen Mixture Adsorption in Metal-Organic Frameworks",
Volume = "110",
Year = "2006",
url = "http://dx.doi.org/10.1021/jp062723w",
doi = "10.1021/jp062723w",
issn = "1520-6106"
}
@article{Feenstra1999,
author = "Feenstra, K. Anton and Hess, Berk and Berendsen, Herman J. C.",
Date-Added = "2018-06-19 20:35:09 +0000",
Date-Modified = "2018-06-19 20:35:52 +0000",
Journal = "Journal of Computational Chemistry",
Number = "8",
Pages = "786--798",
Title = "Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems",
Volume = "20",
Year = "1999",
url = "http://dx.doi.org/10.1002/(sici)1096-987x(199906)20:8<786::aid-jcc5>3.0.co;2-b",
doi = "10.1002/(sici)1096-987x(199906)20:8<786::aid-jcc5>3.0.co;2-b",
issn = "0192-8651"
}
@article{Bjelkmar2010,
author = {Bjelkmar, P\"ar and Larsson, Per and Cuendet, Michel A. and Hess, Berk and Lindahl, Erik},
Date-Added = "2018-06-19 20:32:41 +0000",
Date-Modified = "2018-06-19 20:33:43 +0000",
Journal = "Journal of Chemical Theory and Computation",
Number = "2",
Pages = "459--466",
Title = "Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models",
Volume = "6",
Year = "2010",
url = "http://dx.doi.org/10.1021/ct900549r",
doi = "10.1021/ct900549r",
issn = "1549-9618"
}
@article{Lemkul2016,
author = "Lemkul, Justin A. and Huang, Jing and Roux, Beno\^it and MacKerell, Jr., Alexander D.",
Date-Added = "2018-06-19 20:27:43 +0000",
Date-Modified = "2018-06-19 20:28:32 +0000",
Journal = "Chemical Reviews",
Number = "9",
Pages = "4983--5013",
Title = "An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications",
Volume = "116",
Year = "2016",
url = "http://dx.doi.org/10.1021/acs.chemrev.5b00505",
doi = "10.1021/acs.chemrev.5b00505",
issn = "0009-2665"
}
@article{Harder2006,
author = "Harder, Edward and Anisimov, Victor M. and Vorobyov, Igor V. and Lopes, Pedro E. M. and Noskov, Sergei Y. and MacKerell, Jr., Alexander D. and Roux, Beno\^it",
Date-Added = "2018-06-19 20:26:27 +0000",
Date-Modified = "2018-06-19 20:27:33 +0000",
Journal = "Journal of Chemical Theory and Computation",
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