MCCCS Towhee: References

MCCCS Towhee: References

Overview

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. The Towhee Code

M. G. Martin; "MCCCS Towhee: a tool for Monte Carlo molecular simulation", Mol. Simulat. 39 1212-1222 (2013).
http://towhee.sourceforge.net

Experimental Data

B. D. Smith; R. Srivastava; "Thermodynamic Data for Pure Compounds: Part A Hydrocarbons and Ketones.", Elsevier: Amsterdam (1986).
B. D. Smith; R. Srivastava; "Thermodynamic Data for Pure Compounds: Part B Halogenated hydrocarbons and alcohols.", Elsevier: Amsterdam (1986).
F. Hensel; W. W. Warren Jr.; "Fluid Metals", Princeton University Press: New Jersey (1999).

Force Fields: 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", J. Phys.: Condens. Matter 16 S2629-S2642 (2004).

Force Fields: Alavi et al. 2005

S. Alavi; J. A. Ripmeester; D. D. Klug; "Molecular-dynamics study of structure II hydrogen clathrates", J. Chem. Phys. 123 024507 (2005).

Force Fields: Amber

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", J. Am. Chem. Soc. 106 765-784 (1984).
S. J. Weiner; P. A. Kollman; D. T. Nguyen; D. A. Case; "An All Atom Force Field for Simulations of Proteins and Nucleic Acids", J. Comp. Chem. 7 230-252 (1986).
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", J. Appl. Phys. 76 2726-2737 (1994).
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", J. Am. Chem. Soc. 117 5179-5197 (1995).

Force Fields: Aqvist Ions

J. Aqvist; "Ion-Water interaction Potentials Derived from Free Energy Perturbation Simulations", J. Phys. Chem. 94 8021-8024 (1990).

Force Fields: Belashchenko 2006

D. K. Belashchenko; "Application of the Embedded Atom Model to Liquid Metals: Liquid Mercury", High Temperature 44 675-686 (2006).

Force Fields: Belashchenko 2013

D. K. Belashchenko; "Application of the Embedded Atom Model to Liquid Mercury" High Temperature 51 40-48 (2013).

Force Fields: Catlow/Faux

R. A. Jackson; C. R. A. Catlow; "Computer Simulation Studies of Zeolite Structure", Mol. Simulat. 1 207-224 (1988).
C. R. A. Catlow; C. M. Freeman; B. Vessal; S. M. Tomlinson; M. Leslie; "Molecular Dynamics Studies of Hydrocarbon Diffusion in Zeolites", J. Chem. Soc. Faraday Trans. 87 1947-1950 (1991).
D. A. Faux, W. Smith; T. R. Forester; "Molecular Dynamics Studies of Hydrated and Dehydrated Na⁺-Zeolite-4A", J. Phys. Chem. B 101 1762-1768 (1997).
N. Raj; G. Sastre; C. R. A. Catlow; "Diffusion of Octane in Silicatlite: A Molecular Dynamics Study", J. Phys. Chem. B 103 11007-11015 (1999).

Force Fields: Charmm

E. Neria; S. Fischer; M. Karplus; "Simulation of Activation Free Energies in Molecular Systems", J. Chem. Phys. 105 1902-1921 (1996).
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", J. Phys. Chem. B 102 3586-3616 (1998).
T. Lazaridis; M. Karplus; "Effective Energy Function for Proteins in Solution", Proteins 35 133-152 (1999).
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", J. Comp. Chem. 21 86-104 (2000).
I. J. Chen; D. Yin; A. D. MacKerell Jr.; "Combined Ab initio/Empirical approach for Optimization of Lennard-Jones Parameters for Polar-Neutral Compounds", J. Comp. Chem. 23 199-213 (2001).

Force Fields: ClayFF

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", J. Phys. Chem. B 108 1255-1266 (2004).

Force Fields: Compass

D. Rigby; H. Sun; B. E. Eichinger; "Computer Simulations of Poly(ethylene oxide): Force Field, PVT Diagram and Cyclization Behaviour", Polymer International 44 311-330 (1997).
H. Sun; D. Rigby; "Polysilxanes: ab initio force field and structural, conformational and thermophysical properties", Spectrochimica Acta Part A 53 1301-1323 (1997).
H. Sun; "COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase Applications-Overview with Details on Alkane and Benzene Compounds", J. Phys. Chem. B 102 7338-7364 (1998).
H. Sun; P. Ren; J. R. Fried; "The COMPASS force field: parameterization and validation for phosphazenes", Computational and Theoretical Polymer Science 8 229-246 (1998).
S. W. Bunte; H. Sun; "Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field", J. Phys. Chem. B 104 2477-2489 (2000).
J. Yang; Y. Ren; A. Tian; H. Sun; "COMPASS Force Field for 14 Inorganic Molecules, He, Ne, Ar, Kr, Xe, H₂, O₂, N₂, NO, CO, CO₂, NO₂, CS₂, and SO₂, in Liquid Phases", J. Phys. Chem. B 104 4951-4957 (2000).
M. J. McQuaid; H. Sun; D. Rigby; "Development and Validation of COMPASS Force Field Parameters for Molecules with Aliphatic Azide Chains", J. Comp. Chem. 25 61-71 (2003).

Force Fields: Coon1987

J. E. Coon; S. Gupta; E. McLaughlin; "Isothermal-Isobaric Molecular Dynamics Simulation of Diatomic Liquids and Their Mixtures", Chem. Phys. 113 43-52 (1987).

Force Fields: Cui1998

S. T. Cui; J. I. Siepmann; H. D. Cochran; P. T. Cummings; "Intermolecular potentials and vapor-liquid phase equilibria of perfluorinated alkanes", Fluid Phase Equilib. 146 51-61 (1998).

Force Fields: Cui2002

J. Cui; J. R. Elliott Jr.; "Phase diagrams for a multistep potential model of n-alkanes by discontinuous molecular dynamics and thermodynamic perturbation theory", J. Chem. Phys. 116 8625-8631 (2002).

Force Fields: Dacnis

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", J. Chem. Phys. 114 7174-7181 (2001).

Force Fields: DREIDING

S. L. Mayo; B. D. Olafson; W. A. Goddard III; "DREIDING: A Generic Force Field for Molecular Simulations", J. Phys. Chem. 94 8897-8909 (1990).

Force Fields: Dubb2004

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", Phys. Rev. Lett. 93 (2004).
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", J. Phys. Chem. B 108 12301-12313 (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", J. Am. Chem. Soc. 126 11377-11386 (2004).

Force Fields: Embedded Atom Method

M. S. Daw; M. I. Baskes; "Semiemperical, Quantum Mechanical Calculation of Hydrogen Embrittlement in Metals", Phys. Rev. Lett. 50 1285-1288 (1983).
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", Phys. Rev. B 33 7983-7991 (1986).
H. S. Lim; C. K. Ong; F. Ercolessi; "Stability of face-centered cubic and icosahedral lead clusters", Surface Science 269/270 1109-1115 (1992).
J. J. Hoyt; J. W. Garvin; E. B. Webb III; M. Asta; "An embedded atom method interatomic potential for the Cu-Pb system", Modelling Simul. Mater. Sci. Eng. 11 1-13 (2003).

Force Fields: Elementary Physical Model (EPM)

J. G. Harris; K. H. Yung; "Carbon Dioxide's Liquid-Vapor Coexistence Curve and Critical Properties As Predicted by a Simple Molecular Model", J. Phys. Chem. 99 12021-12024 (1995).

Force Fields: Elliott 2002 (Elli2002)

J. R. Elliott Jr.; "Optimized step potential models for n-alkanes and benzene", Fluid Phase Equilib. 194-197 161-168 (2002).

Force Fields: FENE bonds

K. Kremer; G. S. Grest; "Dynamics of entangled linear polymer melts: A molecular-dynamics simulation", J. Chem. Phys. 92 5057-5086 (1990).

Force Fields: Frischknecht and Curro 2003

A. L. Frischknecht; J. G. Curro; "Improved United Atom Force Field for Poly(dimethylsiloxane)", Macromolecules 36 2122-2129 (2003).

Force Fields: Frischknecht and Martin 2008

A. L. Frischknecht; M. G. Martin; "Simulation of the Adsorption of Nucleotide Monophosphates on Carbon Nanotubes in Aqueous Solution", J. Phys. Chem. C 112 6271-6278 (2008).
T. Werder; J. H. Walther; R. L. Jaffe; T. Halicioglu; P. Koumoutsakos; "On the Water-Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes", J. Phys. Chem. B 107 1345-1352 (2003).

Force Fields: Galassi and Tildesley 1994

G. Galassi; D. J. Tildesley; "Phase Diagrams of Diatomic Molecules Using the Gibbs Ensemble Monte Carlo Method", Mol. Simulat. 13 11-24 (1994).

Force Fields: Gordon

P. A. Gordon; "Development of intermolecular potentials for predicting transport properties of hydrocarbons", J. Chem. Phys 125 014504 (2006).

Force Fields: Gromos

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.
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", J. Phys. Chem. A 103 3596-3607 (1999).

Force Fields: KBFF

S. Weerasinghe; P. E. Smith; "Kirkwood-Buff derived force field for mixtures of acetone and water", J. Chem. Phys. 118 10663-10670 (2003).

Force Fields: Jaramillo

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", J. of Phys. Chem. B. 105 12319-12329 (2001).

Force Fields: Kramer-Farragher-van Beest-van Santen

B. W. H. van Beest; G. J. Kramer; R. A. van Santen; "Force Fields for Silicas and Aluminophosphates Based on Ab Initio Calculations", Phys. Rev. Lett. 64 1955-1958 (1990).
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 ab initio calculations", Phys. Rev. B 43 5068-5080 (1991).

Force Fields: Lybrand-Ghosh-McCammon Ions

T. P. Lybrand; I. Ghosh; J. A. McCammon; "Hydration of Chloride and Bromide Anions: Determination of Relative Free Energy by Computer Simulation", J. Am. Chem. Soc. 107 7793-7794 (1985).

Force Fields: Mendelev et al. 2003 Iron

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", Phil. Mag. 83 3977-3994 (2003).

Force Fields: MCY1976

O. Matsuoka; E. Clementi; M. Yoshimine; "CI study of the water dimer potential surface", J. Chem. Phys. 64 1351-1361 (1976).

Force Fields: MM2

N. L. Allinger; "Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V₁ and V₂ Torsional Terms", J. Am. Chem. Soc. 99 8127-8134 (1977).

Force Fields: MMFF94

T. A. Halgren; "Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94", J. Comp. Chem. 5 & 6 490-519 (1996).
T. A. Halgren; "Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions", J. Comp. Chem. 5 & 6 520-552 (1996).
T. A. Halgren; "Merck Molecular Force Field. III. Molecular Geometries and Vibrational Frequencies for MMFF94", J. Comp. Chem. 5 & 6 553-586 (1996).
T. A. Halgren; R. B. Nachbar; "Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94", J. Comp. Chem. 5 & 6 587-615 (1996).
T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 Using Experimental Data, Additional Computational Data, and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996).
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", J. Comp. Chem. 7 730-748 (1999).

Force Fields: Morrow and Maginn 2002

T. I. Morrow; E. J. Maginn; "Molecular Dynamics Study of the Ionic Liquid 1-n-Butyl-3-methylimidazolium Hexafluorophosphate", J. Phys. Chem. B 106 12807-12813 (2002).
T. I. Morrow; E. J. Maginn; "2002, Vol. 106B", J. Phys. Chem. B 107 9160-9160 (2003).

Force Fields: NERD (all versions)

S. K. Nath; F. A. Escobedo; J. J. de Pablo; "On the simulation of vapor-liquid equilibria for alkanes", J. Chem. Phys. 108 9905-9911 (1998).
S. K. Nath; J. J. de Pablo; "Simulation of vapour-liquid equilibria for branched alkanes", Mol. Phys. 98 231-238 (2000).
S. K. Nath; B. J. Banaszak; J. J. de Pablo; "A new united atom force field for alpha-olefins", J. Chem. Phys. 114 3612-3616 (2001).
S. K. Nath; R. Khare; "New forcefield parameters for branched hydrocarbons", J. Chem. Phys. 115 10837-10844 (2001).
S. K. Nath; "Molecular Simulation of Vapor-Liquid Phase Equilibria of Hydrogen Sulfide and Its Mixtures with Alkanes", J. Phys. Chem. B 107 9498-9504 (2003).
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", J. Phys. Chem. B 108 10071-10076 (2004).

Force Fields: OPLS and TIP*P

W. L. Jorgensen; J. Chandrasekhar; J. D. Madura; R. W. Impey; M. L. Klein; "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79 926-935 (1983).
J. Chandrasekhar; D. Spellmeyer; W. L. Jorgensen; "Energy component analysis for dilute aqueous solutions of Li+, Na+, F- and Cl- Ions", J. Am. Chem. Soc. 106 903-910 (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", J. Am. Chem. Soc. 106 5104-5112 (1984).
W. L. Jorgensen; J. D. Madura; C. J. Swenson; "Optimized Intermolecular Potential Functions for Liquid Hydrocarbons", J. Am. Chem. Soc. 106 6638-6646 (1984).
W. L. Jorgensen; C. J. Swenson; "Optimized Intermolecular Potential Functions for Amides and Peptides. Structure and Properties of Liquid Amides", J. Am. Chem. Soc. 107 569-578 (1985).
W. L. Jorgensen; "Optimized Intermolecular Potential Functions for Liquid Alcohols", J. Phys. Chem. 90 1276-1284 (1986).
W. L. Jorgensen; "Intermolecular Potential Functions and Monte Carlo Simulations for Liquid Sulfur Compounds", J. Phys. Chem. 90 6379-6388 (1986).
W. L. Jorgensen; J. M. Briggs; "Monte Carlo simulations of liquid acetonitrile with a three-site model", Mol. Phys. 63 547-558 (1988).
W. L. Jorgensen; J. M. Briggs; M. L. Contreras; "Relative Partition Coefficients for Organic Solutes from Fluid Simulations", J. Phys. Chem. 94 1683-1686 (1990).
J. Pranata; S. G. Wierschke; W. L. Jorgensen; "OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform", J. Am. Chem. Soc. 113 2810-2819 (1991).
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", J. Phys. Chem. 98 13077-13082 (1994).
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", J. Am. Chem. Soc. 118 11225-11236 (1996). {see the supporting information}
W. L. Jorgensen; "OPLS all-atom parameters for organic molecules, ions, & nucleic acids 12/96", available by sending an email to W. L. Jorgensen.
W. Damm; A. Frontera; J. Tirado-Rives; W. L. Jorgensen; "OPLS all-atom force field for carbohydrates", J. Comp. Chem. 18 1955-1970 (1997).
W. L. Jorgensen; N. A. McDonald; "Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes", J. Mol. Structure Theochem 424 145-155 (1998).
N. A. McDonald; W. L. Jorgensen; "Development of an all-atom force field for heterocycles. Properties of liquid pyrrole, furan, diazoles, and oxazoles", J. Phys. Chem. B 102 8049-8059 (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", J. Am. Chem. Soc. 120, 5104-5111 (1998).
R. C. Rizzo; W. L. Jorgensen; "OPLS all-atom model for amines: resolution of the amine hydration problem", J. Am. Chem. Soc. 121 4827-4836 (1999).
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", J. Chem. Phys. 112 8910-8922 (2000).
W. L. Jorgensen; "OPLS all-atom parameters for organic molecules, ions, & nucleic acids 5/01", available by sending an email to W. L. Jorgensen.
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", J. Phys. Chem. B 105 6474-6487 (2001).

Force Fields: Panagiotopoulos 1989 noble gasses

C. G. Gray; K. E. Gubbins; "Theory of Molecular Fluids Volume 1: Fundamentals" Clarendon Press Oxford (1984).
A. Z. Panagiotopoulos; "Exact Calculations of Fluid-Phase Equilibria by Monte Carlo Simulation in a New Statistical Ensemble", Int. J. Thermophys. 10 447-457 (1989).

Force Fields: 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", Mol. Phys. 92 825-833 (1997).

Force Fields: QMFF-VIII

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", J. Comp. Chem. 22 1782-1800 (2001).

Force Fields: 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", J. Porous Mater. 2 43-49 (1995).

Force Fields: Shah and Maginn 2002

J. K. Shah; E. J. Maginn; "A Monte Carlo simulation study of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate: liquid structure, volumetric properties and infinite dilution solution thermodynamics of CO₂" Fluid Phase Equilib. 222-223 195-203 (2004).

Force Fields: Shukla 1987

K. P. Shukla; "Thermodynamic properties of simple fluid mixtures from perturbation theory", Mol. Phys. 62 1143-1163 (1987).

Force Fields: SKS n-alkanes

B. Smit; S. Karaborni; J. I. Siepmann; "Computer simulations of vapor-liquid phase equilibria of n-alkanes", J. Chem. Phys. 102 2126-2140 (1995).
B. Smit; S. Karaborni; J. I. Siepmann; "Erratum: Computer simulations of vapor-liquid phase equilibria of n-alkanes [J. Chem. Phys. 102, 2126 (1995)]", J. Chem. Phys. 109 (1998).

Force Fields: Simple Point Charge - Extended

H. J. C. Berendsen; J. R. Grigera; T. P. Straatsma; "The Missing Term in Effective Pair Potentials", J. Phys. Chem. 91 6269-6271 (1987).

Force Fields: SMMK

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", Faraday Discuss. 104 17-36 (1996).
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", Mol. Phys. 90 687-693 (1997).

Force Fields: Smith and Dang 1994

D. E. Smith; L. X. Dang; "Computer simulations of NaCl association in polarizable water", J. Chem. Phys. 100 3757-3766 (1994).

Force Fields: Stillinger-Weber Potential

F. H. Stillinger; T. A. Weber; "Computer simulation of local order in condensed phases of silicon", Phys. Rev. B 31 5262-5271 (1985).
K. Ding; H. C. Andersen; "Molecular-dynamics simulation of amorphous germanium", Phys. Rev. B 34 6987-6991 (1986).
R. L. C. Vink; G. T. Barkema; W. F. van der Weg; N. Mousseau; "Fitting the Stillinger-Weber potential to amorphous silicon", Journal of Non-crystalline Solids 282 248-255 (2001).

Force Fields: 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", J. Phys. Chem. B 107 14443-14451 (2003).

Force Fields: Teleman et al. 1987

O. Teleman; B. Jonsson; S. Engstrom; "A molecular dynamics simulation of a water model with intramolecular degrees of freedom", Mol. Phys. 60 193-203 (1987).

Force Fields: TraPPE

M. G. Martin; J. I. Siepmann; "Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes", J. Phys. Chem. B 102 2569-2577 (1998).
M. G. Martin; J. I. Siepmann; "Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations", Theor. Chem. Acc. 99 347-350 (1998).
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", J. Phys. Chem. B 103 4508-4517 (1999).
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", J. Phys. Chem. B 104 8008-8016 (2000).
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", J. Phys. Chem. B 105 3090-3104 (2001).
J. Potoff; J. I. Siepmann; "Vapor-Liquid Equilibria of Mixtures Containing Alkanes, Carbon Dioxide, and Nitrogen", AIChE J. 47 1676-1682 (2001).
G. Kamath; F. Cao; J. J. Potoff; "An Improved Force Field for the Prediction of the Vapor-Liquid Equilibria for Carboxylic Acids", J. Phys. Chem. B 108 14130-14136 (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", J. Phys. Chem. B 108 17596-17605 (2004).
G. Kamath; J. Robinson; J. J. Potoff; "Application of the TraPPE-UA force field for determination of vapor-liquid equilibria of carboxylate esters", Fluid Phase Equilib. 240 46-55 (2006).

Force Fields: Universal Force Field (UFF)

A. K. Rappe; W. A. Goddard III; "Charge Equilibration for Molecular Dynamics Simulations", J. Phys. Chem. 95 3358-3363 (1991).
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", J. Am. Chem. Soc. 114 10024-10035 (1992).

Force Fields: Vega et al. 1992 (Vega1992)

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", J. Chem. Phys. 96 2296-2305 (1992).

Force Fields: Walther et al. 2001 (Walt2001)

J. H. Walther; R. Jaffe; T. Halicioglu; P. Koumoutsakos; "Carbon Nanotubes in Water: Structural Characteristics and Energetics", J. Phys. Chem. B 105 9980-9987 (2001).

Force Fields: Wielopolski and Smith 1985 (Wielop1985)

P. A. Wielopolski; E. R. Smith; "Molecular dynamics studies of dielectric behaviour and orientational correlations of liquid ethylene oxide (oxirane)", Mol. Phys. 54 467-478 (1985).

Functional Forms: Surface Potentials

W. A. Steele; "The Physical Interaction of Gases With Crystalline Solids", Surf. Sci. 36 317-352 (1973).
C. Lastoskie; K. E. Gubbins; N. Quirke; "Pore Size Heterogeneity and the Carbon Slit Pore: A Density Functional Theory Model", Langmuir 9 2693-2702 (1993).
J. B. Hooper; J. D. McCoy; J. G. Curro; "Density functional theory of simple polymers in a slit pore. I. Theory and efficient algorithm.", J. Chem. Phys. 112 3090-3093 (2000).

Methods: Charge Assignment

J. Gasteiger; M. Marsili; "Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access To Atomic Charges", Tetrahedron 36 3219-3288 (1980).

Methods: Configurational-bias

J. I. Siepmann; "A method for the direct calculation of chemical potentials for dense chain systems", Mol. Phys. 70 1145-1158 (1990).
J. I. Siepmann; D. Frenkel; "Configurational bias Monte Carlo: a new sampling scheme for flexible chains", Mol. Phys. 75 59-70 (1992).
G. C. A. M. Mooij; D. Frenkel; B. Smit; "Direct simulation of phase equilibria of chain molecules", J. Phys.: Condens. Matter 4 L255-L259 (1992).
D. Frenkel; G. C. A. M. Mooij; B. Smit; "Novel scheme to study structural and thermal properties of continuously deformable molecules", J. Phys.: Condens. Matter 4 3053-3076 (1992).
M. Laso; J. J. de Pablo; U. W. Suter; "Simulation of phase equilibria for chain molecules", J. Chem. Phys. 97 2817-2819 (1992).
J. I. Siepmann; I. R. McDonald; "Monte Carlo simulations of mixed monolayers", Mol. Phys. 75 255-259 (1992).
T. J. H. Vlugt; M. G. Martin; B. Smit; J. I. Siepmann; R. Krishna; "Improving the efficiency of the configurational-bias Monte Carlo algorithm", Mol. Phys. 94 727-733 (1998).
T. J. H. Vlugt; R. Krishna; B. Smit; "Molecular Simulations of Adsorption Isotherms for Linear and Branched Alkanes and Their Mixtures in Silicalite" J. Phys. Chem. B 103 1102-1118 (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", J. Phys. Chem. B 103 4508-4517 (1999).
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", Macromolecules 33 7207-7218 (2000).
M. G. Martin; A. P. Thompson; "Industrial property prediction using Towhee and LAMMPS" Fluid Phase Equilib. 217 105-110 (2004).
M. G. Martin; M. J. Biddy; "Monte Carlo Molecular Simulation Predictions for the Heat of Vaporization of Acetone and Butyramide", Fluid Phase Equilib. 236 53-57 (2005).
M. G. Martin; A. L. Frischknecht; "Using arbitrary trial distributions to improve intramolecular sampling in configurational-bias Monte Carlo", Mol. Phys. 104 2439-2456 (2006).

Methods: Energy Biasing

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" J. Phys. Chem. 97 13742 (1993).

Methods: Ensembles

N. Metropolis; A. W. Rosenbluth; M. N. Rosenbluth; A. H. Teller; E. Teller; "Equation of State Calculations by Fast Computing Machines", J. Chem. Phys. 21 1087-1092 (1953).
G. E. Norman; V. S. Filinov; "Investigations of Phase Transitions by a Monte-Carlo Method", High Temperature 7 216-222 (1969).

I. R. McDonald; "NpT-ensemble Monte Carlo calculations for binary liquid mixtures", Mol. Phys. 23 41-58 (1972).
L. A. Rowley; D. Nicholson; N. G. Parsonage; "Monte Carlo Grand Canonical Ensemble Calculation in a Gas-Liquid Transition Region for 12-6 Argon", J. Comp. Phys. 17 401-414 (1975).
A. Z. Panagiotopoulos; "Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble", Mol. Phys. 61 813-826 (1987).
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", Mol. Phys. 63 527-545 (1988).
B. Smit; Ph. de Smedt; D. Frenkel; "Computer simulations in the Gibbs ensemble", Mol. Phys. 68 931-950 (1989).
S. Yashonath; C. N. R. Rao; "A Monte Carlo study of crystal structure transformations", Mol. Phys. 54 245-251 (1985).

Methods: Ewald Sum and Electrostatics

P. P. Ewald; "Die Berchnung optischer und elektrostatischer Gitterpotentiale" Ann. Phys. 64 253-287 (1921)
M. J. L. Sangster; M. Dixon; "Interionic potentials in alkali halides and their use in simulations of the molten salts", Advances in Physics 25 247-343 (1976).
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", J. Phys. Chem. B 101 3017-3020 (1997).

Methods: General Simulation

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).
M. G. Martin; "Simulation of Phase Equlibria", Ph.D. Thesis, University of Minnesota (1999).

Methods: Histogram Reweighting

A. M. Ferrenberg; R. H. Swendsen; "Optimized Monte Carlo Data Analysis", Phys. Rev. Lett. 63 1195-1198 (1989).
R. H. Swendsen; "Modern methods of analyzing Monte Carlo computer simulations", Physica A 194 53-62 (1993).
J. J. Potoff; A. Z. Panagiotopoulos; "Critical point and phase behavior of the pure fluid and a Lennard-Jones mixture". J. Chem. Phys. 109 10914-10920 (1998).
A. Z. Panagiotopoulos; "Monte Carlo methods for phase equilibria of fluids", J. Phys.: Condens. Matter 12 R25-R52 (2000).

Methods: Mixing Rules

M. Waldman; A. T. Hagler; "New Combining Rules for Rare Gas van der Waals Parameters", J. Comp. Chem. 14 1077-1084 (1993).
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", Chem. Phys. Lett. 222 529-539 (1994).
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", J. Chem. Phys. 119 5740-5761 (2003).
J. D.. Weeks; D. Chandler; H. C. Andersen; "Role of repulsive forces in determinig the equilibrium structure of simple liquids." J. Chem. Phys, 54, 5237-5247 (1971)

Methods: Monte Carlo Moves (other than configurational-bias)

M. Lal; "Monte Carlo Computer Simulation of Chain Molecules. I", Mol. Phys. 17 57-64 (1969).
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", Mol. Phys. 71 931-943 (1990).
L. R. Dodd; T. D. Boone; D. N. Theodorou; "A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses", Mol. Phys. 78 961-996 (1993).
B. Chen; J. I. Siepmann; "A Novel Monte Carlo Algorithm for Simulating Strongly Associating Fluids: Applications to Water, Hydrogen Fluoride, and Acetic Acid", J. Phys. Chem. B 104 8725-8734 (2000).
B. Chen; J. I. Siepmann; "Improving the Efficiency of the Aggregation-Volume-Bias Monte Carlo Algorithm", J. Phys. Chem. B 105 11275-11282 (2001).

Methods: Pressure

W. R. Smith; D. Henderson; Y. Tago; "Mean spherical approximation and optimized cluster theory for the square-well fluid", J. Chem. Phys. 67 5308-5316 (1977).
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" J. Chem. Phys. 109 2791-2797 (1998).

Methods: Random Number Generators

F. James; "A review of pseudorandom number generators", Comp. Phys. Comm. 60 329-344 (1990).
F. James; "RANLUX: A Fortran implementation of the high-quality pseudorandom number generator of Luscher", Comp. Phys. Comm. 79 111-114 (1994). See http://www.astro.multivax.de:8000/phillip/ranlux.txt for the subroutines associated with this reference.
M. Lüscher; "A portable high-quality random number generator for lattice field theory simulations", Comp. Phys. Comm. 79 100-110 (1994).
P. l'Ecuyer; "Good Parameters and Implementations for Combined Multiple Random Number Generators", Operations Research 47 159-164 (1999).
L.-Y. Deng; "Efficient and Portable Multiple Recursive Generators of Large Order", ACM Transactions on Modeling and Computer Simulation 15 1-13 (2005).

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Last updated: July 22, 2021 Send comments to: Marcus Martin