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<title>MCCCS Towhee (references)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS Towhee (references)</font></b></font></div>
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<td width="700" valign="top"> <b>Overview</b>
<ul>
This section contains references to papers and books that are either the source materials for the methods or force fields in Towhee, or are helpful
reviews of those subjects. The references are arranged by subject, date of publication, and then alphabetical by author.
</ul>
<a name="introduction"><b>The Towhee Code</b></a>
<ul>
<li><a name="website">
http://towhee.sourceforge.net</a>
</li>
</ul>
<a name="experimental_data"><b>Experimental Data</b></a>
<ul>
<li><a name="smith_srivastava_1986">
B. D. Smith; R. Srivastava;
"Thermodynamic Data for Pure Compounds: Part A Hydrocarbons and Ketones.",
Elsevier: Amsterdam (1986).
</a></li>
<li><a name="smith_srivastava_1986">
B. D. Smith; R. Srivastava;
"Thermodynamic Data for Pure Compounds: Part B Halogenated hydrocarbons and alcohols.",
Elsevier: Amsterdam (1986).
</a></li>
<li><a name="hensel_warren_1999">
F. Hensel; W. W. Warren Jr.;
"Fluid Metals",
Princeton University Press: New Jersey (1999).
</a></li>
</ul>
<a name="force_fields_ackl2004"><b>Force Fields: Ackland <i>et al.</i> 2004</b></a>
<ul>
<li><a name="ackland_et_al_2004">
G. J. Ackland; M. I. Mendelev; D. J. Srolovitz; S. Han; A. V. Barashev;
"Development of an interatomic potential for phosphorus impurities in alpha-iron",
<i>J. Phys.: Condens. Matter</i> <b>16</b> S2629-S2642 (2004).
</a></li>
</ul>
<a name="force_fields_alavi2005"><b>Force Fields: Alavi <i>et al.</i> 2005</b></a>
<ul>
<li><a name="alavi_et_al_2005">
S. Alavi; J. A. Ripmeester; D. D. Klug;
"Molecular-dynamics study of structure II hydrogen clathrates",
<i>J. Chem. Phys.</i> <b>123</b> 024507 (2005).
</a></li>
</ul>
<a name="force_fields_amber"><b>Force Fields: Amber</b></a>
<ul>
<li><a name="weiner_et_al_1984">
S. J. Weiner; P. A. Kollman; D. A. Case; U. C. Singh; C. Ghio; G. Alagona; S. Profeta Jr.; P. Weiner;
"A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins",
<i>J. Am. Chem. Soc.</i> <b>106</b> 765-784 (1984).
</a></li>
<li><a name="weiner_et_al_1986">
S. J. Weiner; P. A. Kollman; D. T. Nguyen; D. A. Case;
"An All Atom Force Field for Simulations of Proteins and Nucleic Acids",
<i>J. Comp. Chem.</i> <b>7</b> 230-252 (1986).
</a></li>
<li><a name="dick_ritchie_1994">
J. J. Dick; J. P. Ritchie;
"Molecular mechanics modeling of shear and the crystal orientation dependence of the elastic precursor shock strength in pentaerythritol tetranitrate",
<i>J. Appl. Phys.</i> <b>76</b> 2726-2737 (1994).
</a></li>
<li><a name="cornell_et_al_1995">
W. D. Cornell; P. Cieplak; C. I. Bayly; I. R. Gould; K. M. Merz Jr.; D. M. Ferguson; D. C. Spellmeyer; T. Fox; J. W. Caldwell; P. A. Kollman;
"A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules",
<i>J. Am. Chem. Soc.</i> <b>117</b> 5179-5197 (1995).
</a></li>
</ul>
<a name="force_fields_aqvist"><b>Force Fields: Aqvist Ions</b></a>
<ul>
<li><a name="aqvist_1990">
J. Aqvist; "Ion-Water interaction Potentials Derived from Free Energy Perturbation Simulations",
<i>J. Phys. Chem. </i> <b>94</b> 8021-8024 (1990).
</a></li>
</ul>
<a name="force_fields_catlow_faux"><b>Force Fields: Catlow/Faux</b></a>
<ul>
<li><a name="jackson_catlow_1988">
R. A. Jackson; C. R. A. Catlow;
"Computer Simulation Studies of Zeolite Structure",
<i>Mol. Sim.</i> <b>1</b> 207-224 (1988).
</a></li>
<li><a name="catlow_et_al_1991">
C. R. A. Catlow; C. M. Freeman; B. Vessal; S. M. Tomlinson; M. Leslie;
"Molecular Dynamics Studies of Hydrocarbon Diffusion in Zeolites",
<i>J. Chem. Soc. Faraday Trans.</i> <b>87</b> 1947-1950 (1991).
</a></li>
<li><a name="faux_et_al_1997">
D. A. Faux, W. Smith; T. R. Forester;
"Molecular Dynamics Studies of Hydrated and Dehydrated Na<sup>+</sup>-Zeolite-4A",
<i>J. Phys. Chem. B</i> <b>101</b> 1762-1768 (1997).
</a></li>
<li><a name="raj_et_al_1999">
N. Raj; G. Sastre; C. R. A. Catlow;
"Diffusion of Octane in Silicatlite: A Molecular Dynamics Study",
<i>J. Phys. Chem. B</i> <b>103</b> 11007-11015 (1999).
</a></li>
</ul>
<a name="force_fields_charmm"><b>Force Fields: Charmm</b></a>
<ul>
<li><a name="neria_et_al_1996">
E. Neria; S. Fischer; M. Karplus;
"Simulation of Activation Free Energies in Molecular Systems",
<i>J. Chem. Phys.</i> <b>105</b> 1902-1921 (1996).
</a></li>
<li><a name="mackerell_et_al_1998">
A. D. MacKerell Jr.; D. Bashford; M. Bellott; R. L. Dunbrack Jr.; J. D. Evanseck; M. J. Field; S. Fischer; J. Gao; H. Guo; S. Ha; D. Joseph-McCarthy;
L. Kuchnir; K. Kuczera; F. T. K. Lau; C. Mattos; S. Michnick; T. Ngo; D. T. Nguyen; B. Prodhom; W. E. Reiher III; B. Roux; M. Schlenkrich; J. C. Smith;
R. Stote; J. Straub; M. Watanabe; J. Wiorkiewicz-Kuczera; D. Yin; M. Karplus;
"All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins",
<i>J. Phys. Chem. B</i> <b>102</b> 3586-3616 (1998).
</a></li>
<li><a name="lazaridis_karplus_1999">
T. Lazaridis; M. Karplus;
"Effective Energy Function for Proteins in Solution",
<i>Proteins</i> <b>35</b> 133-152 (1999).
</a></li>
<li><a name="foloppe_mackerell_2000">
N. Foloppe; A. D. MacKerell Jr.;
"All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data",
<i>J. Comp. Chem.</i> <b>21</b> 86-104 (2000).
</a></li>
<li><a name="Chen_2001">
I. J. Chen; D. Yin; A. D. MacKerell Jr.;
"Combined Ab initio/Empirical approach for Optimization of Lennard-Jones Parameters for Polar-Neutral Compounds",
<i>J. Comp. Chem.</i> <b>23</b> 199-213 (2001).
</a></li>
</ul>
<a name="force_fields_clayff"><b>Force Fields: ClayFF</b></a>
<ul>
<li><a name="cygan_et_al_2004">
R. T. Cygan; J.-J. Liang; A. G. Kalinichev;
"Molecular Models of Hydroxide, Oxyhydroxide, and Clay Phases and the Development of a General Force Field",
<i>J. Phys. Chem. B</i> <b>108</b> 1255-1266 (2004).
</a></li>
</ul>
<a name="force_fields_compass"><b>Force Fields: Compass</b></a>
<ul>
<li><a name="rigby_et_al_1997">
D. Rigby; H. Sun; B. E. Eichinger;
"Computer Simulations of Poly(ethylene oxide): Force Field, PVT Diagram and Cyclization Behaviour",
<i>Polymer International</i> <b>44</b> 311-330 (1997).
</a></li>
<li><a name="sun_rigby_1997">
H. Sun; D. Rigby;
"Polysilxanes: ab initio force field and structural, conformational and thermophysical properties",
<i>Spectrochimica Acta Part A</i> <b>53</b> 1301-1323 (1997).
</a></li>
<li><a name="sun_1998">
H. Sun;
"COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase Applications-Overview with Details on Alkane and Benzene Compounds",
<i>J. Phys. Chem. B</i> <b>102</b> 7338-7364 (1998).
</a></li>
<li><a name="sun_et_al_1998">
H. Sun; P. Ren; J. R. Fried;
"The COMPASS force field: parameterization and validation for phosphazenes",
<i>Computational and Theoretical Polymer Science</i> <b>8</b> 229-246 (1998).
</a></li>
<li><a name="bunte_sun_2000">
S. W. Bunte; H. Sun;
"Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field",
<i>J. Phys. Chem. B</i> <b>104</b> 2477-2489 (2000).
</a></li>
<li><a name="yang_et_al_2000">
J. Yang; Y. Ren; A. Tian; H. Sun;
"COMPASS Force Field for 14 Inorganic Molecules, He, Ne, Ar, Kr, Xe, H<sub>2</sub>, O<sub>2</sub>, N<sub>2</sub>, NO, CO, CO<sub>2</sub>,
NO<sub>2</sub>, CS<sub>2</sub>, and SO<sub>2</sub>, in Liquid Phases",
<i>J. Phys. Chem. B</i> <b>104</b> 4951-4957 (2000).
</a></li>
<li><a name="mcquaid_et_al_2003">
M. J. McQuaid; H. Sun; D. Rigby;
"Development and Validation of COMPASS Force Field Parameters for Molecules with Aliphatic Azide Chains",
<i>J. Comp. Chem.</i> <b>25</b> 61-71 (2003).
</a></li>
</ul>
<a name="force_fields_coon1987"><b>Force Fields: Coon1987</b></a>
<ul>
<li><a name="coon_et_al_1987">
J. E. Coon; S. Gupta; E. McLaughlin;
"Isothermal-Isobaric Molecular Dynamics Simulation of Diatomic Liquids and Their Mixtures",
<i>Chem. Phys.</i> <b>113</b> 43-52 (1987).
</a></li>
</ul>
<a name="force_fields_cui1998"><b>Force Fields: Cui1998</b></a>
<ul>
<li><a name="cui_et_al_1998">
S. T. Cui; J. I. Siepmann; H. D. Cochran; P. T. Cummings;
"Intermolecular potentials and vapor-liquid phase equilibria of perfluorinated alkanes",
<i>Fluid Phase Equilib.</i> <b>146</b> 51-61 (1998).
</a></li>
</ul>
<a name="force_fields_cui2002"><b>Force Fields: Cui2002</b></a>
<ul>
<li><a name="cui_elliott_2002">
J. Cui; J. R. Elliott Jr.;
"Phase diagrams for a multistep potential model of <i>n</i>-alkanes by discontinuous molecular dynamics and thermodynamic perturbation theory",
<i>J. Chem. Phys.</i> <b>116</b> 8625-8631 (2002).
</a></li>
</ul>
<a name="force_fields_dacnis"><b>Force Fields: Dacnis</b></a>
<ul>
<li><a name="martin_et_al_2001">
M. G. Martin; A. P. Thompson; T. M. Nenoff;
"Effect of pressure, membrane thickness, and placement of control volumes on the flux of methane through thin silicalite membranes: A dual control
volume grand canonical molecular dynamics study",
<i>J. Chem. Phys.</i> <b>114</b> 7174-7181 (2001).
</a></li>
</ul>
<a name="force_fields_dreiding"><b>Force Fields: DREIDING</b></a>
<ul>
<li><a name="mayo_et_al_1990">
S. L. Mayo; B. D. Olafson; W. A. Goddard III;
"DREIDING: A Generic Force Field for Molecular Simulations",
<i>J. Phys. Chem.</i> <b>94</b> 8897-8909 (1990).
</a></li>
</ul>
<a name="force_fields_dubb2004"><b>Force Fields: Dubb2004</b></a>
<ul>
<li><a name="dubbeldam_et_al_2004_prl">
D. Dubbeldam; S. Calero; T. J. H. Vlugt; R. Krishna; T. L. M. Maesen; E. Beerdsen; B. Smit;
"Force Field Parametrization through Fitting on Inflection Points in Isotherms",
<i>Phys. Rev. Lett.</i> <b>93</b> (2004).
</a></li>
<li><a name="dubbeldam_et_al_2004_jpcb">
D. Dubbeldam; S. Calero; T. J. H. Vlugt; R. Krishna; T. L. M. Maesen; B. Smit;
"United Atom Force Field for Alkanes in Nanoporous Materials",
<i>J. Phys. Chem. B</i> <b>108</b> 12301-12313 (2004).
</a></li>
<li><a name="calero_et_al_2004">
S. Calero; D. Dubbeldam; R. Krishna; B. Smit; T. J. H. Vlugt; J. F. M. Denayer; J. A. Martens; T. L. M. Maesen;
"Understanding the Role of Sodium during Adsorption: A Force Field for Alkanes in Sodium-Exchanged Faujasites",
<i>J. Am. Chem. Soc.</i> <b>126</b> 11377-11386 (2004).
</a></li>
</ul>
<a name="force_fields_eam"><b>Force Fields: Embedded Atom Method</b></a>
<ul>
<li><a name="daw_baskes_1983">
M. S. Daw; M. I. Baskes;
"Semiemperical, Quantum Mechanical Calculation of Hydrogen Embrittlement in Metals",
<i>Phys. Rev. Lett.</i> <b>50</b> 1285-1288 (1983).
</a></li>
<li><a name="foiles_et_al_1986">
S. M. Foiles; M. I. Baskes; M. S. Daw;
"Embedded-atom-method functions for the fcc metals Cu, Ag, Au, Ni, Pd, Pt, and their alloys",
<i>Phys. Rev. B</i> <b>33</b> 7983-7991 (1986).
</a></li>
<li><a name="lim_et_al_1992">
H. S. Lim; C. K. Ong; F. Ercolessi;
"Stability of face-centered cubic and icosahedral lead clusters",
<i>Surface Science</i> <b>269/270</b> 1109-1115 (1992).
</a></li>
<li><a name="hoyt_et_al_2003">
J. J. Hoyt; J. W. Garvin; E. B. Webb III; M. Asta;
"An embedded atom method interatomic potential for the Cu-Pb system",
<i>Modelling Simul. Mater. Sci. Eng.</i> <b>11</b> 1-13 (2003).
</a></li>
</ul>
<a name="force_fields_epm"><b>Force Fields: Elementary Physical Model (EPM)</b></a>
<ul>
<li><a name="harris_yung_1995">
J. G. Harris; K. H. Yung;
"Carbon Dioxide's Liquid-Vapor Coexistence Curve and Critical Properties As Predicted by a Simple Molecular Model",
<i>J. Phys. Chem.</i> <b>99</b> 12021-12024 (1995).
</a></li>
</ul>
<a name="force_fields_elli2002"><b>Force Fields: Elliott 2002 (Elli2002)</b></a>
<ul>
<li><a name="elliott_2002">
J. R. Elliott Jr.;
"Optimized step potential models for <i>n</i>-alkanes and benzene",
<i>Fluid Phase Equilib.</i> <b>194-197</b> 161-168 (2002).
</a></li>
</ul>
<a name="force_fields_fris2003"><b>Force Fields: Frischknecht and Curro 2003</b></a>
<ul>
<li><a name="frischknecht_curro_2003">
A. L. Frischknecht; J. G. Curro;
"Improved United Atom Force Field for Poly(dimethylsiloxane)",
<i>Macromolecules</i> <b>36</b> 2122-2129 (2003).
</a></li>
</ul>
<a name="force_fields_gala1994"><b>Force Fields: Galassi and Tildesley 1994</b></a>
<ul>
<li><a name="galassi_tildesley_1994">
G. Galassi; D. J. Tildesley;
"Phase Diagrams of Diatomic Molecules Using the Gibbs Ensemble Monte Carlo Method",
<i>Mol. Sim.</i> <b>13</b> 11-24 (1994).
</a></li>
</ul>
<a name="force_fields_gromos"><b>Force Fields: Gromos</b></a>
<ul>
<li><a name="van_gunsteren_et_al_1996">
W. F. van Gunsteren; S. R. Billeter; A. A. Eising; P. H. Hunenberger; P. Kruger; A. E. Mark; W. R. P. Scott; I. G. Tironi;
"Biomolecular Simulation: The GROMOS96 Manual and User Guide.",
VdF: Hochschulverlag AG an der ETH Zurich and BIOMOS b.v, Zurich, Gronigen (1996). ISBN 3 7281 2422 2.
</a></li>
<li><a name="scott_et_al_1999">
W. R. P. Scott; P. H. Hunenberger; I. G. Tironi; A. E. Mark; S. R. Billeter; J. Fennen; A. E. Torda; T. Huber; P. Kruger; W. F. van Gunsteren;
"The GROMOS Biomolecular Simulation Program Package",
<i>J. Phys. Chem. A</i> <b>103</b> 3596-3607 (1999).
</a></li>
</ul>
<a name="force_fields_jaramillo"><b>Force Fields: Jaramillo</b></a>
<ul>
<li><a name="jaramillo_et_al_2001">
E. Jaramillo; C. P. Grey; S. M. Auerbach;
"Molecular Dynamics Studies of Hydrofluorocarbons in Faujasite-type Zeolites: Modeling Guest-Induced Cation Migration in Dry Zeolites",
<i>J. of Phys. Chem. B.</i> <b>105</b> 12319-12329 (2001).
</a></li>
</ul>
<a name="force_fields_kfvbvs"><b>Force Fields: Kramer-Farragher-van Beest-van Santen</b></a>
<ul>
<li><a name="vanbeest_et_al_1990">
B. W. H. van Beest; G. J. Kramer; R. A. van Santen;
"Force Fields for Silicas and Aluminophosphates Based on <i>Ab Initio</i> Calculations",
<i>Phys. Rev. Lett.</i> <b>64</b> 1955-1958 (1990).
</a></li>
<li><a name="kramer_et_al_1991">
G. J. Kramer; N. P. Farragher; B. W. H. van Beest; R. A. van Santen;
"Interatomic force fields for silicas, aluminophosphates, and zeolites: Derivation based on <i>ab initio</i> calculations",
<i>Phys. Rev. B</i> <b>43</b> 5068-5080 (1991).
</a></li>
</ul>
<a name="force_fields_lgm"><b>Force Fields: Lybrand-Ghosh-McCammon Ions</b></a>
<ul>
<li><a name="lybrand_et_al_1985">
T. P. Lybrand; I. Ghosh; J. A. McCammon;
"Hydration of Chloride and Bromide Anions: Determination of Relative Free Energy by Computer Simulation",
<i>J. Am. Chem. Soc.</i> <b>107</b> 7793-7794 (1985).
</a></li>
</ul>
<a name="force_fields_mend2003"><b>Force Fields: Mendelev <i>et al.</i> 2003 Iron</b></a>
<ul>
<li><a name="mendelev_et_al_2003">
M. I. Mendelev; S. Han; D. J. Srolovitz; G. J. Ackland; D. Y. Sun; M. Asta;
"Development of new interactomic potentials appropriate for crystalline and liquid iron",
<i>Phil. Mag.</i> <b>83</b> 3977-3994 (2003).
</a></li>
</ul>
<a name="force_fields_mcy1976"><b>Force Fields: MCY1976</b></a>
<ul>
<li><a name="matsuoka_et_al_1976">
O. Matsuoka; E. Clementi; M. Yoshimine;
"CI study of the water dimer potential surface",
<i>J. Chem. Phys.</i> <b>64</b> 1351-1361 (1976).
</a></li>
</ul>
<a name="force_fields_mm2"><b>Force Fields: MM2</b></a>
<ul>
<li><a name="allinger_1977">
N. L. Allinger;
"Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V<sub>1</sub> and V<sub>2</sub> Torsional Terms",
<i>J. Am. Chem. Soc.</i> <b>99</b> 8127-8134 (1977).
</a></li>
</ul>
<a name="force_fields_mmff94"><b>Force Fields: MMFF94</b></a>
<ul>
<li><a name="halgren_jcc_1996_I">
T. A. Halgren;
"Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94",
<i>J. Comp. Chem.</i> <b>5 & 6</b> 490-519 (1996).
</a></li>
<li><a name="halgren_jcc_1996_II">
T. A. Halgren;
"Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions",
<i>J. Comp. Chem.</i> <b>5 & 6</b> 520-552 (1996).
</a></li>
<li><a name="halgren_jcc_1996_III">
T. A. Halgren;
"Merck Molecular Force Field. III. Molecular Geometries and Vibrational Frequencies for MMFF94",
<i>J. Comp. Chem.</i> <b>5 & 6</b> 553-586 (1996).
</a></li>
<li><a name="halgren_nachbar_jcc_1996">
T. A. Halgren; R. B. Nachbar;
"Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94",
<i>J. Comp. Chem.</i> <b>5 & 6</b> 587-615 (1996).
</a></li>
<li><a name="halgren_jcc_1996_V">
T. A. Halgren;
"Merck Molecular Force Field. V. Extension of MMFF94 Using Experimental Data, Additional Computational Data, and Empirical Rules",
<i>J. Comp. Chem.</i> <b>5 & 6</b> 616-641 (1996).
</a></li>
<li><a name="halgren_jcc_1999">
T. A. Halgren;
"MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction
Energies and Geometries",
<i>J. Comp. Chem.</i> <b>7</b> 730-748 (1999).
</a></li>
</ul>
<a name="force_fields_morrow2002"><b>Force Fields: Morrow and Maginn 2002</b></a>
<ul>
<li><a name="morrow_maginn_2002">
T. I. Morrow; E. J. Maginn;
"Molecular Dynamics Study of the Ionic Liquid 1-<i>n</i>-Butyl-3-methylimidazolium Hexafluorophosphate",
<i>J. Phys. Chem. B</i> <b>106</b> 12807-12813 (2002).
</a></li>
<li><a name="morrow_maginn_2003">
T. I. Morrow; E. J. Maginn;
"2002, Vol. 106B",
<i>J. Phys. Chem. B</i> <b>107</b> 9160-9160 (2003).
</a></li>
</ul>
<a name="force_fields_nerd"><b>Force Fields: NERD (all versions)</b></a>
<ul>
<li><a name="nath_et_al_1998">
S. K. Nath; F. A. Escobedo; J. J. de Pablo;
"On the simulation of vapor-liquid equilibria for alkanes",
<i>J. Chem. Phys.</i> <b>108</b> 9905-9911 (1998).
</a></li>
<li><a name="nath_depablo_2000">
S. K. Nath; J. J. de Pablo;
"Simulation of vapour-liquid equilibria for branched alkanes",
<i>Mol. Phys.</i> <b>98</b> 231-238 (2000).
</a></li>
<li><a name="nath_et_al_2001">
S. K. Nath; B. J. Banaszak; J. J. de Pablo;
"A new united atom force field for alpha-olefins",
<i>J. Chem. Phys.</i> <b>114</b> 3612-3616 (2001).
</a></li>
<li><a name="nath_khare_2001">
S. K. Nath; R. Khare;
"New forcefield parameters for branched hydrocarbons",
<i>J. Chem. Phys.</i> <b>115</b> 10837-10844 (2001).
</a></li>
<li><a name="nath_2003">
S. K. Nath;
"Molecular Simulation of Vapor-Liquid Phase Equilibria of Hydrogen Sulfide and Its Mixtures with Alkanes",
<i>J. Phys. Chem. B</i> <b>107</b> 9498-9504 (2003).
</a></li>
<li><a name="khare_et_al_2004">
R. Khare; A. K. Sum; S. K. Nath; J. J. de Pablo;
"Simulation of Vapor-Liquid Phase Equilibria of Primary Alcohols and Alchol-Alkane Mixtures",
<i>J. Phys. Chem. B</i> <b>108</b> 10071-10076 (2004).
</a></li>
</ul>
<a name="force_fields_opls"><b>Force Fields: OPLS and TIP*P</b></a>
<ul>
<li><a name="jorgensen_et_al_1983">
W. L. Jorgensen; J. Chandrasekhar; J. D. Madura; R. W. Impey; M. L. Klein;
"Comparison of simple potential functions for simulating liquid water",
<i>J. Chem. Phys.</i> <b>79</b> 926-935 (1983).
</a></li>
<li><a name="chandrasekhar_et_al_1984">
J. Chandrasekhar; D. Spellmeyer; W. L. Jorgensen;
"Energy component analysis for dilute aqueous solutions of Li+, Na+, F- and Cl- Ions",
<i>J. Am. Chem. Soc.</i> <b>106</b> 903-910 (1984).
</a></li>
<li><a name="cournoyer_jorgensen_1984">
M. E. Cournoyer; W. L. Jorgensen;
"Solvent Effects on the Relative Energies of Carbonium Ions. Solvation and Internal Rotation for the Allyl Cation in Liquid Hydrogen Fluoride",
<i>J. Am. Chem. Soc.</i> <b>106</b> 5104-5112 (1984).
</a></li>
<li><a name="jorgensen_et_al_1984">
W. L. Jorgensen; J. D. Madura; C. J. Swenson;
"Optimized Intermolecular Potential Functions for Liquid Hydrocarbons",
<i>J. Am. Chem. Soc.</i> <b>106</b> 6638-6646 (1984).
</a></li>
<li><a name="jorgensen_swenson_1985">
W. L. Jorgensen; C. J. Swenson;
"Optimized Intermolecular Potential Functions for Amides and Peptides. Structure and Properties of Liquid Amides",
<i>J. Am. Chem. Soc.</i> <b>107</b> 569-578 (1985).
</a></li>
<li><a name="jorgensen_1986_alcohol">
W. L. Jorgensen;
"Optimized Intermolecular Potential Functions for Liquid Alcohols",
<i>J. Phys. Chem.</i> <b>90</b> 1276-1284 (1986).
</a></li>
<li><a name="jorgensen_1986_sulfur">
W. L. Jorgensen;
"Intermolecular Potential Functions and Monte Carlo Simulations for Liquid Sulfur Compounds",
<i>J. Phys. Chem.</i> <b>90</b> 6379-6388 (1986).
</a></li>
<li><a name="jorgensen_briggs_1988">
W. L. Jorgensen; J. M. Briggs;
"Monte Carlo simulations of liquid acetonitrile with a three-site model",
<i>Mol. Phys.</i> <b>63</b> 547-558 (1988).
</a></li>
<li><a name="jorgensen_et_al_1990">
W. L. Jorgensen; J. M. Briggs; M. L. Contreras;
"Relative Partition Coefficients for Organic Solutes from Fluid Simulations",
<i>J. Phys. Chem.</i> <b>94</b> 1683-1686 (1990).
</a></li>
<li><a name="pranata_et_al_1991">
J. Pranata; S. G. Wierschke; W. L. Jorgensen;
"OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform",
<i>J. Am. Chem. Soc.</i> <b>113</b> 2810-2819 (1991).
</a></li>
<li><a name="kaminski_et_al_1994">
G. Kaminski; E. M. Duffy; T. Matsui; W. L. Jorgensen;
"Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all-atom model",
<i>J. Phys. Chem.</i> <b>98</b> 13077-13082 (1994).
</a></li>
<li><a name="jorgensen_et_al_1996">
W. L. Jorgensen; D. S. Maxwell; J. Tirado-Rives;
"Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids",
<i>J. Am. Chem. Soc.</i> <b>118</b> 11225-11236 (1996). {see the supporting information}
</a></li>
<li><a name="jorgensen_per_com_1996">
W. L. Jorgensen;
"OPLS all-atom parameters for organic molecules, ions, & nucleic acids 12/96",
available by sending an email to W. L. Jorgensen.
</a></li>
<li><a name="damm_et_al_1997">
W. Damm; A. Frontera; J. Tirado-Rives; W. L. Jorgensen;
"OPLS all-atom force field for carbohydrates",
<i>J. Comp. Chem.</i> <b>18</b> 1955-1970 (1997).
</a></li>
<li><a name="jorgensen_mcdonald_1998">
W. L. Jorgensen; N. A. McDonald;
"Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes",
<i>J. Mol. Structure Theochem</i> <b>424</b> 145-155 (1998).
</a></li>
<li><a name="mcdonald_jorgensen_1998">
N. A. McDonald; W. L. Jorgensen;
"Development of an all-atom force field for heterocycles. Properties of liquid pyrrole, furan, diazoles, and oxazoles",
<i>J. Phys. Chem. B</i> <b>102</b> 8049-8059 (1998).
</a></li>
<li><a name="mcdonald_et_al_1998">
N. A. McDonald; E. M. Duffy; W. L. Jorgensen;
"Monte Carlo investigations of selective anion complexation by a bis(phenylurea)p-tert-butylcalix[4]arene",
<i>J. Am. Chem. Soc.</i> <b>120</b>, 5104-5111 (1998).
</a></li>
<li><a name="rizzo_jorgensen_2000">
R. C. Rizzo; W. L. Jorgensen;
"OPLS all-atom model for amines: resolution of the amine hydration problem",
<i>J. Am. Chem. Soc.</i> <b>121</b> 4827-4836 (1999).
</a></li>
<li><a name="mahoney_jorgensen_2000">
M. W. Mahoney; W. L. Jorgensen;
"A five-site model for liquid water and the reproduction of the density anomoly by rigid, nonpolarizable potential functions",
<i>J. Chem. Phys.</i> <b>112</b> 8910-8922 (2000).
</a></li>
<li><a name="jorgensen_per_com_2001">
W. L. Jorgensen;
"OPLS all-atom parameters for organic molecules, ions, & nucleic acids 5/01",
available by sending an email to W. L. Jorgensen.
</a></li>
<li><a name="kaminski_et_al_2001">
G. A. Kaminski; R. A. Friesner; J. Tirado-Rives; W. L. Jorgensen;
"Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides",
<i>J. Phys. Chem. B</i> <b>105</b> 6474-6487 (2001).
</a></li>
</ul>
<a name="force_fields_pana1989"><b>Force Fields: Panagiotopoulos 1989 noble gasses</b></a>
<ul>
<li><a name="gray_gubbins_1984">
C. G. Gray; K. E. Gubbins;
"Theory of Molecular Fluids Volume 1: Fundamentals"
<i>Clarendon Press</i> <b>Oxford</b> (1984).
</a></li>
<li><a name="panagiotopoulos_1989">
A. Z. Panagiotopoulos;
"Exact Calculations of Fluid-Phase Equilibria by Monte Carlo Simulation in a New Statistical Ensemble",
<i>Int. J. Thermophys.</i> <b>10</b> 447-457 (1989).
</a></li>
</ul>
<a name="force_fields_potter1997"><b>Force Fields: Potter <i>et al.</i> 1997</b></a>
<ul>
<li><a name="potter_et_al_1997">
S. C. Potter; D. J. Tildesley; A. N. Burgess; S. C. Rogers;
"A transferable potential model for the liquid-vapour equilibria of fluoromethanes",
<i>Mol. Phys.</i> <b>92</b> 825-833 (1997).
</a></li>
</ul>
<a name="force_fields_qmff_viii"><b>Force Fields: QMFF-VIII</b></a>
<ul>
<li><a name="ewig_et_al_2001">
C. S. Ewig; R. Berry; U. Dinur; J.-R. Hill; M.-J. Hwang; H. Li; C. Liang; J. Maple; Z. Peng; T. P. Stockfisch; T. S. Thacher; L. Yan; X. Ni;
A. T. Hagler;
"Derivation of Class II Force Fields. VIII. Derivation of a General Quantum Mechanical Force Field for Organic Compounds",
<i>J. Comp. Chem.</i> <b>22</b> 1782-1800 (2001).
</a></li>
</ul>
<a name="force_fields_richar1995"><b>Force Fields: Richards <i>et al.</i> 1995</b></a>
<ul>
<li><a name="richards_et_al_1995">
A. J. Richards; K. Watanabe; N. Austin; M. R. Stapleton;
"Computer Simulation of the Gas Separation Properties of Zeolite Li-X",
<i>J. Porous Mater.</i> <b>2</b> 43-49 (1995).
</a></li>
</ul>
<a name="force_fields_shah2004"><b>Force Fields: Shah and Maginn 2002</b></a>
<ul>
<li><a name="shah_maginn_2004">
J. K. Shah; E. J. Maginn;
"A Monte Carlo simulation study of the ionic liquid 1-<i>n</i>-butyl-3-methylimidazolium hexafluorophosphate: liquid structure, volumetric properties
and infinite dilution solution thermodynamics of CO<sub>2</sub>"
<i>Fluid Phase Equilib.</i> <b>222-223</b> 195-203 (2004).
</a></li>
</ul>
<a name="force_fields_sks"><b>Force Fields: Shukla 1987</b></a>
<ul>
<li><a name="shukla_1987">
K. P. Shukla;
"Thermodynamic properties of simple fluid mixtures from perturbation theory",
<i>Mol. Phys.</i> <b>62</b> 1143-1163 (1987).
</a></li>
</ul>
<a name="force_fields_sks"><b>Force Fields: SKS n-alkanes</b></a>
<ul>
<li><a name="smit_et_al_1995">
B. Smit; S. Karaborni; J. I. Siepmann;
"Computer simulations of vapor-liquid phase equilibria of <i>n</i>-alkanes",
<i>J. Chem. Phys.</i> <b>102</b> 2126-2140 (1995).
</a></li>
<li><a name="smit_et_al_erratum_1998">
B. Smit; S. Karaborni; J. I. Siepmann;
"Erratum: Computer simulations of vapor-liquid phase equilibria of <i>n</i>-alkanes [J. Chem. Phys. 102, 2126 (1995)]",
<i>J. Chem. Phys.</i> <b>109</b> (1998).
</a></li>
</ul>
<a name="force_fields_spce"><b>Force Fields: Simple Point Charge - Extended</b></a>
<ul>
<li><a name="berendsen_et_al_1987">
H. J. C. Berendsen; J. R. Grigera; T. P. Straatsma;
"The Missing Term in Effective Pair Potentials",
<i>J. Phys. Chem.</i> <b>91</b> 6269-6271 (1987).
</a></li>
</ul>
<a name="force_fields_smmk"><b>Force Fields: SMMK </b></a>
<ul>
<li><a name="mundy_et_al_1996">
C. J. Mundy; S. Balasubramanian; K. Bagchi; J. I. Siepmann; M. L. Klein;
"Equilibrium and non-equilibrium simulation studies of fluid alkanes in bulk and at interfaces",
<i>Faraday Discuss.</i> <b>104</b> 17-36 (1996).
</a></li>
<li><a name="siepmann_et_al_1997">
J. I. Siepmann; M. G. Martin; C. J. Mundy; M. L. Klein;
"Intermolecular potentials for branched alkanes and the vapour-liquid phase equilibria of n-heptane, 2-methylhexane, and 3-ethylpentane",
<i>Mol. Phys.</i> <b>90</b> 687-693 (1997).
</a></li>
</ul>
<a name="force_fields_smith1994"><b>Force Fields: Smith and Dang 1994 </b></a>
<ul>
<li><a name="smith_dang_1994">
D. E. Smith; L. X. Dang;
"Computer simulations of NaCl association in polarizable water",
<i>J. Chem. Phys.</i> <b>100</b> 3757-3766 (1994).
</a></li>
</ul>
<a name="force_fields_stillinger_weber"><b>Force Fields: Stillinger-Weber Potential</b></a>
<ul>
<li><a name="stillinger_weber_1985">
F. H. Stillinger; T. A. Weber;
"Computer simulation of local order in condensed phases of silicon",
<i>Phys. Rev. B</i> <b>31</b> 5262-5271 (1985).
</a></li>
<li><a name="ding_andersen_1986">
K. Ding; H. C. Andersen;
"Molecular-dynamics simulation of amorphous germanium",
<i>Phys. Rev. B</i> <b>34</b> 6987-6991 (1986).
</a></li>
<li><a name="vink_et_al_2001">
R. L. C. Vink; G. T. Barkema; W. F. van der Weg; N. Mousseau;
"Fitting the Stillinger-Weber potential to amorphous silicon",
<i>Journal of Non-crystalline Solids</i> <b>282</b> 248-255 (2001).
</a></li>
</ul>
<a name="force_fields_sum2003"><b>Force Fields: Sum <i>et al.</i> 2003</b></a>
<ul>
<li><a name="sum_et_al_2003">
A. K. Sum; M. J. Biddy; J. J. de Pablo; M. J. Tupy;
"Predictive Molecular Model for the Thermodynamic and Transport Properties of Triacylglycerols",
<i>J. Phys. Chem. B</i> <b>107</b> 14443-14451 (2003).
</a></li>
</ul>
<a name="force_fields_tele1987"><b>Force Fields: Teleman <i>et al.</i> 1987</b></a>
<ul>
<li><a name="teleman_et_al_1987">
O. Teleman; B. Jonsson; S. Engstrom;
"A molecular dynamics simulation of a water model with intramolecular degrees of freedom",
<i>Mol. Phys.</i> <b>60</b> 193-203 (1987).
</a></li>
</ul>
<a name="force_fields_trappe"><b>Force Fields: TraPPE</b></a>
<ul>
<li><a name="martin_siepmann_1998_jpcb">
M. G. Martin; J. I. Siepmann;
"Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes",
<i>J. Phys. Chem. B</i> <b>102</b> 2569-2577 (1998).
</a></li>
<li><a name="martin_siepmann_1998_tca">
M. G. Martin; J. I. Siepmann;
"Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations",
<i>Theor. Chem. Acc.</i> <b>99</b> 347-350 (1998).
</a></li>
<li><a name="martin_siepmann_1999">
M. G. Martin; J. I. Siepmann;
"Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. united-atom description of
branched alkanes",
<i>J. Phys. Chem. B</i> <b>103</b> 4508-4517 (1999).
</a></li>
<li><a name="wick_et_al_2000">
C. D. Wick; M. G. Martin; J. I. Siepmann;
"Transferable potentials for phase equilibria. 4. United-atom description of linear and branched alkenes and alkylbenzenes",
<i>J. Phys. Chem. B</i> <b>104</b> 8008-8016 (2000).
</a></li>
<li><a name="chen_et_al_2001">
B. Chen; J. Potoff; J. I. Siepmann;
"Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of
primary, secondary, and tertiary alcohols",
<i>J. Phys. Chem. B</i> <b>105</b> 3090-3104 (2001).
</a></li>
<li><a name="potoff_siepmann_2001">
J. Potoff; J. I. Siepmann;
"Vapor-Liquid Equilibria of Mixtures Containing Alkanes, Carbon Dioxide, and Nitrogen",
<i>AIChE J.</i> <b>47</b> 1676-1682 (2001).
</a></li>
<li><a name="kamath_et_al_2004">
G. Kamath; F. Cao; J. J. Potoff;
"An Improved Force Field for the Prediction of the Vapor-Liquid Equilibria for Carboxylic Acids",
<i>J. Phys. Chem. B</i> <b>108</b> 14130-14136 (2004).
</a></li>
<li><a name="stubbs_et_al_2004">
J. M. Stubbs; J. J. Potoff; J. I. Siepmann;
"Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes",
<i>J. Phys. Chem. B</i> <b>108</b> 17596-17605 (2004).
</a></li>
</ul>
<a name="force_fields_uff"><b>Force Fields: Universal Force Field (UFF)</b></a>
<ul>
<li><a name="rappe_goddard_1991">
A. K. Rappe; W. A. Goddard III;
"Charge Equilibration for Molecular Dynamics Simulations",
<i>J. Phys. Chem.</i> <b>95</b> 3358-3363 (1991).
</a></li>
<li><a name="rappe_et_al_1992">
A. K. Rappe; C. J. Casewit; K. S. Colwell; W. A. Goddard III; W. M. Skiff;
"UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations",
<i>J. Am. Chem. Soc.</i> <b>114</b> 10024-10035 (1992).
</a></li>
</ul>
<a name="force_fields_vega1992"><b>Force Fields: Vega <i>et al.</i> 1992 (Vega1992)</b></a>
<ul>
<li><a name="vega_et_al_1992">
L. Vega; E. de Miguel; L. F. Rull; G. Jackson; I. A. McLure;
"Phase equilibria and critical behavior of square-well fluids of variable width by Gibbs ensemble Monte Carlo simulation",
<i>J. Chem. Phys.</i> <b>96</b> 2296-2305 (1992).
</a></li>
</ul>
<a name="force_fields_walt2001"><b>Force Fields: Walther <i>et al.</i> 2001 (Walt2001)</b></a>
<ul>
<li><a name="walther_et_al_2001">
J. H. Walther; R. Jaffe; T. Halicioglu; P. Koumoutsakos;
"Carbon Nanotubes in Water: Structural Characteristics and Energetics",
<i>J. Phys. Chem. B</i> <b>105</b> 9980-9987 (2001).
</a></li>
</ul>
<a name="functional_forms_umbrella"><b>Functional Forms: Surface Potentials</b></a>
<ul>
<li><a name="steele_1973">
W. A. Steele;
"The Physical Interaction of Gases With Crystalline Solids",
<i>Surf. Sci.</i> <b>36</b> 317-352 (1973).
</a></li>
<li><a name="lastoskie_et_al_1993">
C. Lastoskie; K. E. Gubbins; N. Quirke;
"Pore Size Heterogeneity and the Carbon Slit Pore: A Density Functional Theory Model",
<i>Langmuir</i> <b>9</b> 2693-2702 (1993).
</a></li>
<li><a name="hooper_et_al_2000">
J. B. Hooper; J. D. McCoy; J. G. Curro;
"Density functional theory of simple polymers in a slit pore. I. Theory and efficient algorithm.",
<i>J. Chem. Phys.</i> <b>112</b> 3090-3093 (2000).
</a></li>
</ul>
<a name="methods_charge_assignment"><b>Methods: Charge Assignment</b></a>
<ul>
<li><a name="gasteiger_marsili_1980">
J. Gasteiger; M. Marsili;
"Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access To Atomic Charges",
<i>Tetrahedron</i> <b>36</b> 3219-3288 (1980).
</a></li>
</ul>
<a name="methods_configurational_bias"><b>Methods: Configurational-bias</b></a>
<ul>
<li><a name="siepmann_1990">
J. I. Siepmann;
"A method for the direct calculation of chemical potentials for dense chain systems",
<i>Mol. Phys.</i> <b>70</b> 1145-1158 (1990).
</a></li>
<li><a name="siepmann_frenkel_1992">
J. I. Siepmann; D. Frenkel;
"Configurational bias Monte Carlo: a new sampling scheme for flexible chains",
<i>Mol. Phys.</i> <b>75</b> 59-70 (1992).
</a></li>
<li><a name="frenkel_et_al_1992">
D. Frenkel; G. C. A. M. Mooij; B. Smit;
"Novel scheme to study structural and thermal properties of continuously deformable molecules",
<i>J. Phys.: Condens. Matter</i> <b>4</b> 3053-3076 (1992).
</a></li>
<li><a name="laso_et_al_1992">
M. Laso; J. J. de Pablo; U. W. Suter;
"Simulation of phase equilibria for chain molecules",
<i>J. Chem. Phys. </i> <b>97</b> 2817-2819 (1992).
</a></li>
<li><a name="siepmann_mcdonald_1992">
J. I. Siepmann; I. R. McDonald;
"Monte Carlo simulations of mixed monolayers",
<i>Mol. Phys.</i> <b>75</b> 255-259 (1992).
</a></li>
<li><a name="vlugt_et_al_1998">
T. J. H. Vlugt; M. G. Martin; B. Smit; J. I. Siepmann; R. Krishna;
"Improving the efficiency of the configurational-bias Monte Carlo algorithm",
<i>Mol. Phys.</i> <b>94</b> 727-733 (1998).
</a></li>
<li><a name="vlugt_et_al_1999">
T. J. H. Vlugt; R. Krishna; B. Smit;
"Molecular Simulations of Adsorption Isotherms for Linear and Branched Alkanes and Their Mixtures in Silicalite"
<i>J. Phys. Chem. B</i> <b>103</b> 1102-1118 (1999).
</a></li>
<li><a name="martin_siepmann_1999">
M. G. Martin; J. I. Siepmann;
"Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. united-atom description of
branched alkanes",
<i>J. Phys. Chem. B</i> <b>103</b> 4508-4517 (1999).
</a></li>
<li><a name="wick_siepmann_2000">
C. D. Wick; J. I. Siepmann;
"Self-Adapting Fixed-End-Point Configurational-Bias Monte Carlo Method for the Regrowth of Interior Segments of Chain Molecules with Strong
Intramolecular Interactions",
<i>Macromolecules</i> <b>33</b> 7207-7218 (2000).
</a></li>
<li><a name="martin_thompson_2004">
M. G. Martin; A. P. Thompson;
"Industrial property prediction using Towhee and LAMMPS"
<i>Fluid Phase Equilib.</i> <b>217</b> 105-110 (2004).
</a></li>
<li><a name="martin_biddy_2005">
M. G. Martin; M. J. Biddy;
"Monte Carlo Molecular Simulation Predictions for the Heat of Vaporization of Acetone and Butyramide",
<i>Fluid Phase Equilib.</i> <b>236</b> 53-57 (2005).
</a></li>
<li><a name="martin_frischknecht_2006">
M. G. Martin; A. L. Frischknecht;
"Using arbitrary trial distributions to improve intramolecular sampling in configurational-bias Monte Carlo",
<i>Mol. Phys.</i> <b>104</b> 2439-2456 (2006).
</a></li>
</ul>
<a name="Energy_Biasing"><b>Methods: Energy Biasing</b></a>
<ul>
<li><a name="snurr_et_al_1993">
R. Q. Snurr; A. T. Bell; D. N. Theodorou;
"Prediction of Adsorption of Aromatic Hydrocarbons in Silicalite from Grand Canonical Monte Carlo Simulations with Biased Insertions"
<i>J. Phys. Chem.</i> <b>97</b> 13742 (1993).
</a></li>
</ul>
<a name="methods_ensembles"><b>Methods: Ensembles</b></a>
<ul>
<li><a name="metropolis_et_al_1953">
N. Metropolis; A. W. Rosenbluth; M. N. Rosenbluth; A. H. Teller; E. Teller;
"Equation of State Calculations by Fast Computing Machines",
<i>J. Chem. Phys.</i> <b>21</b> 1087-1092 (1953).
</a></li>
<li><a name="norman_1969">
G. E. Norman; V. S. Filinov;
"Investigations of Phase Transitions by a Monte-Carlo Method",
<i>High Temperature</i> <b>7</b> 216-222 (1969).
</li>
<li><a name="mcdonald_1972">
I. R. McDonald;
"NpT-ensemble Monte Carlo calculations for binary liquid mixtures",
<i>Mol. Phys.</i> <b>23</b> 41-58 (1972).
</a></li>
<li><a name="rowley_et_al_1975">
L. A. Rowley; D. Nicholson; N. G. Parsonage;
"Monte Carlo Grand Canonical Ensemble Calculation in a Gas-Liquid Transition Region for 12-6 Argon",
<i>J. Comp. Phys.</i> <b>17</b> 401-414 (1975).
</a></li>
<li><a name="panagiotopoulos_1987">
A. Z. Panagiotopoulos;
"Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble",
<i>Mol. Phys.</i> <b>61</b> 813-826 (1987).
</a></li>
<li><a name="panagiotopoulos_et_al_1988">
A. Z. Panagiotopoulos; N. Quirke; M. Stapleton; D. J. Tildesley;
"Phase equilibria by simulation in the Gibbs ensemble. Alternative derivation, generalization and application to mixture and membrane equilibria",
<i>Mol. Phys.</i> <b>63</b> 527-545 (1988).
</a></li>
<li><a name="smit_et_al_1989">
B. Smit; Ph. de Smedt; D. Frenkel;
"Computer simulations in the Gibbs ensemble",
<i>Mol. Phys.</i> <b>68</b> 931-950 (1989).
</a></li>
<li><a name="yashonath_rao_1985">
S. Yashonath; C. N. R. Rao;
"A Monte Carlo study of crystal structure transformations",
<i>Mol. Phys.</i> <b>54</b> 245-251 (1985).
</a></li>
</ul>
<a name="methods_ewald_sum"><b>Methods: Ewald Sum and Electrostatics</b></a>
<ul>
<li><a name="ewald_1921">
P. P. Ewald;
<i>Ann. Phys.</i> <b>64</b> 253 (1921)
</a></li>
<li><a name="sangster_dixon_1976">
M. J. L. Sangster; M. Dixon;
"Interionic potentials in alkali halides and their use in simulations of the molten salts",
<i>Advances in Physics</i> <b>25</b> 247-343 (1976).
</a></li>
<li><a name="hummer_et_al_1997">
G. Hummer; L. R. Pratt; A. E. Garcia; B. J. Berne; S. W. Rick;
"Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules",
<i>J. Phys. Chem. B</i> <b>101</b> 3017-3020 (1997).
</a></li>
</ul>
<a name="methods_general_simulation"><b>Methods: General Simulation</b></a>
<ul>
<li><a name="allen_and_tildesley">
M. P. Allen; D. J. Tildesley;
"Computer Simulation of Liquids",
Oxford Science Publications: New York (1987 - and many reprintings), ISBN 0 19 855645 4(Paperback).
</a></li>
<li><a name="martin_thesis_1999">
M. G. Martin;
"Simulation of Phase Equlibria",
Ph.D. Thesis, University of Minnesota (1999).
</a></li>
</ul>
<a name="methods_histogram_reweighting"><b>Methods: Histogram Reweighting</b></a>
<ul>
<li><a name="ferrenberg_swendsen_1989">
A. M. Ferrenberg; R. H. Swendsen;
"Optimized Monte Carlo Data Analysis",
<i>Phys. Rev. Lett.</i> <b>63</b> 1195-1198 (1989).
</a></li>
<li><a name="swendsen_1993">
R. H. Swendsen;
"Modern methods of analyzing Monte Carlo computer simulations",
<i>Physica A</i> <b>194</b> 53-62 (1993).
</a></li>
<li><a name="potoff_panagiotopoulos_1998">
J. J. Potoff; A. Z. Panagiotopoulos;
"Critical point and phase behavior of the pure fluid and a Lennard-Jones mixture".
<i>J. Chem. Phys.</i> <b>109</b> 10914-10920 (1998).
</a></li>
<li><a name="panagiotopoulos_2000">
A. Z. Panagiotopoulos;
"Monte Carlo methods for phase equilibria of fluids",
<i>J. Phys.: Condens. Matter </i> <b>12</b> R25-R52 (2000).
</a></li>
</ul>
<a name="methods_mixing_rules"><b>Methods: Mixing Rules</b></a>
<ul>
<li><a name="waldman_hagler_1993">
M. Waldman; A. T. Hagler;
"New Combining Rules for Rare Gas van der Waals Parameters",
<i>J. Comp. Chem.</i> <b>14</b> 1077-1084 (1993).
</a></li>
<li><a name="beutler_et_al_1994">
T. C. Beutler; A. E. Mark; R. C. van Schaik; P. R. Gerber; W. F. van Gunsteren;
"Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations",
<i>Chem. Phys. Lett.</i> <b>222</b> 529-539 (1994).
</a></li>
<li><a name="shirts_et_al_2003">
M. R. Shirts; J. W. Pitera; W. C. Swope; V. S. Pande;
"Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins",
<i>J. Chem. Phys.</i> <b>119</b> 5740-5761 (2003).
</a></li>
<li><a name="weeks_et_al_1970">
J. D.. Weeks; D. Chandler; H. C. Andersen;
"Role of repulsive forces in determinig the equilibrium structure of simple liquids."
<i>J. Chem. Phys</i>, <b>54</b>, 5237-5247 (1971)
</a></li>
</ul>
<a name="methods_monte_carlo_moves"><b>Methods: Monte Carlo Moves (other than configurational-bias)</b></a>
<ul>
<li><a name="lal_1969">
M. Lal;
"Monte Carlo Computer Simulation of Chain Molecules. I",
<i>Mol. Phys.</i> <b>17</b> 57-64 (1969).
</a></li>
<li><a name="cracknell_et_al_1990">
R. F. Cracknell; D. Nicholson; N. G. Parsonage; H. Evans;
"Rotational insertion bias: a novel method for simulating dense phases of structured particles, with particular application to water",
<i>Mol. Phys.</i> <b>71</b> 931-943 (1990).
</a></li>
<li><a name="dodd_et_al_1993">
L. R. Dodd; T. D. Boone; D. N. Theodorou;
"A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses",
<i>Mol. Phys.</i> <b>78</b> 961-996 (1993).
</a></i>
<li><a name="chen_siepmann_2000">
B. Chen; J. I. Siepmann;
"A Novel Monte Carlo Algorithm for Simulating Strongly Associating Fluids: Applications to Water, Hydrogen Fluoride, and Acetic Acid",
<i>J. Phys. Chem. B</i> <b>104</b> 8725-8734 (2000).
</a></li>
<li><a name="chen_siepmann_2001">
B. Chen; J. I. Siepmann;
"Improving the Efficiency of the Aggregation-Volume-Bias Monte Carlo Algorithm",
<i>J. Phys. Chem. B</i> <b>105</b> 11275-11282 (2001).
</a></li>
</ul>
<a name="methods_pressure"><b>Methods: Pressure</b></a>
<ul>
<li><a name="smith_et_al_1977">
W. R. Smith; D. Henderson; Y. Tago;
"Mean spherical approximation and optimized cluster theory for the square-well fluid",
<i>J. Chem. Phys.</i> <b>67</b> 5308-5316 (1977).
</a></li>
<li><a name="hummer_et_al_1998">
G. Hummer; N. Gronbech-Jensen; M. Neumann;
"Pressure calculation in polar and charged systems using Ewald summation: Results for the extended simple point charge model of water"
<i>J. Chem. Phys.</i> <b>109</b> 2791-2797 (1998).
</a></li>
</ul>
<a name="methods_random_number_generators"><b>Methods: Random Number Generators</b></a>
<ul>
<li><a name="james_1990">
F. James;
"A review of pseudorandom number generators",
<i>Comp. Phys. Comm.</i> <b>60</b> 329-344 (1990).
</a></li>
<li><a name="james_1994">
F. James;
"RANLUX: A Fortran implementation of the high-quality pseudorandom number generator of Luscher",
<i>Comp. Phys. Comm.</i> <b>79</b> 111-114 (1994).
See <a href="http://www.astro.multivax.de:8000/phillip/ranlux.txt">http://www.astro.multivax.de:8000/phillip/ranlux.txt</a> for the
subroutines associated with this reference.
</a></li>
<li><a name="luscher_1994">
M. Lüscher;
"A portable high-quality random number generator for lattice field theory simulations",
<i>Comp. Phys. Comm.</i> <b>79</b> 100-110 (1994).
</a></li>
<li><a name="lecuyer_1999">
P. l'Ecuyer;
"Good Parameters and Implementations for Combined Multiple Random Number Generators",
<i>Operations Research</i> <b>47</b> 159-164 (1999).
</a></li>
<li><a name="deng_2005">
L.-Y. Deng;
"Efficient and Portable Multiple Recursive Generators of Large Order",
<i>ACM Transactions on Modeling and Computer Simulation</i> <b>15</b> 1-13 (2005).
</a></li>
</ul>
<a href="index.html">Return to the main towhee web page</a>
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<i><font size="2">Send comments to:
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<a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a><br></br>
<i>Last updated:</i> <!-- #BeginDate format:Am1 -->August 17, 2011<!-- #EndDate -->
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