--- trunk/electrostaticMethodsPaper/electrostaticMethods.bib 2006/01/28 22:42:46 2575 +++ trunk/electrostaticMethodsPaper/electrostaticMethods.bib 2006/03/13 22:59:52 2612 @@ -1,2519 +1,2317 @@ -@string{jcp = "J. Chem. Phys."} -@string{cpl = "Chem. Phys. Lett."} -@string{jpc = "J. Phys. Chem."} -@string{jpcA = "J. Phys. Chem. A"} -@string{jpcB = "J. Phys. Chem. B"} -@string{cp = "Chem. Phys."} -@string{acp = "Adv. Chem. Phys."} -@string{pra = "Phys. Rev. A"} -@string{prb = "Phys. Rev. B"} -@string{pre = "Phys. Rev. E"} -@string{prl = "Phys. Rev. Lett."} -@string{rmp = "Rev. Mod. Phys."} -@string{jml = "J. Mol. Liq."} -@string{mp = "Mol. Phys."} -@string{pnas = "Proc. Natl. Acad. Sci. USA"} -@string{jacs = "J. Am. Chem. Soc."} -@string{jcc = "J. Comput. Chem."} -@string{pccp = "Phys. Chem. Chem. Phys."} +%% This BibTeX bibliography file was created using BibDesk. +%% http://bibdesk.sourceforge.net/ -@Book{Berne90, - author = {B.~J. Berne and R. Pecora}, - title = {Dynamic Light Scattering}, - publisher = {Robert E. Krieger Publishing Company, Inc.}, - year = 1990, - address = {Malabar, Florida} -} -@Article{Evans77, - author = {D.~J. Evans}, - title = {On the representation of orientation space}, - journal = {Mol. Phys.}, - year = 1977, - volume = 34, - pages = {317-325} -} +%% Created for Chris Fennell at 2006-03-13 17:01:21 -0500 -@Article{Tuckerman92, - author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna}, - title = {Reversible multiple time scale molecular dynamics}, - journal = jcp, - year = 1992, - volume = 97, - pages = {1990-2001} -} -@Book{Hansen86, - author = {J.~P. Hansen and I.~R. McDonald}, - title = {Theory of Simple Liquids}, - chapter = 7, - publisher = {Academic Press}, - year = 1986, - address = {London}, - pages = {199-206} -} +%% Saved with string encoding Western (ASCII) -@Article{Angelani98, - author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani}, - title = {Connected Network of Minima as a Model Glass: Long - Time Dynamics}, - journal = prl, - year = 1998, - volume = 81, - number = 21, - pages = {4648-4651} -} -@Article{Stillinger82, - author = {F.~H. Stillinger and T.~A. Weber}, - title = {Hidden structure in liquids}, - journal = pra, - year = 1982, - volume = 25, - number = 2, - pages = {978-989} -} +@STRING{acp = "Adv. Chem. Phys."} -@Article{Stillinger83, - author = {F.~H. Stillinger and T.~A. Weber}, - title = {Dynamics of structural transitions in liquids}, - journal = pra, - year = 1983, - volume = 28, - number = 4, - pages = {2408-2416} -} +@STRING{cp = "Chem. Phys."} -@Article{Weber84, - author = {T.~A. Weber and F.~H. Stillinger}, - title = {The effect of density on the inherent structure in - liquids}, - journal = jcp, - year = 1984, - volume = 80, - number = 6, - pages = {2742-2746} -} +@STRING{cpl = "Chem. Phys. Lett."} -@Article{Stillinger85, - author = {F.~H. Stillinger and T.~A. Weber}, - title = {Inherent structure theory of liquids in the - hard-sphere limit}, - journal = jcp, - year = 1985, - volume = 83, - number = 9, - pages = {4767-4775} -} +@STRING{jacs = "J. Am. Chem. Soc."} -@Article{Stillinger98, - author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger}, - title = {Signatures of distinct dynamical regimes in the - energy landscape of a glass-forming liquid}, - journal = {Nature}, - year = 1998, - volume = 393, - pages = {554-557} -} +@STRING{jcc = "J. Comput. Chem."} +@STRING{jcp = "J. Chem. Phys."} -@Article{Parkhurst75a, - author = {H.~J. {Parkhurst, Jr.} and J. Jonas}, - title = {Dense liquids. I. The effect of density and - temperature on viscosity of tetramethylsilane and - benzene-$\mbox{D}_6$}, - journal = jcp, - year = 1975, - volume = 63, - number = 6, - pages = {2698-2704} -} +@STRING{jml = "J. Mol. Liq."} -@Article{Parkhurst75b, - author = {H.~J. {Parkhurst, Jr.} and J. Jonas}, - title = {Dense liquids. II. The effect of density and - temperature on viscosity of tetramethylsilane and - benzene }, - journal = jcp, - year = 1975, - volume = 63, - number = 6, - pages = {2705-2709} -} +@STRING{jpc = "J. Phys. Chem."} -@Article{Forester97, - author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke}, - title = {Antibiotic activity of valinomycin - Molecular - dynamics simulations involving the water/membrane - interface}, - journal = {J. Chem. Soc. - Faraday Transactions}, - year = 1997, - volume = 93, - pages = {613-619} -} +@STRING{jpca = "J. Phys. Chem. A"} -@Article{Tieleman98, - author = {D.~P. Tieleman and H.~J.~C. Berendsen}, - title = {A molecular dynamics study of the pores formed by - Escherichia coli OmpF porin in a fully hydrated - palmitoyloleoylphosphatidylcholine bilayer}, - journal = {Biophys. J.}, - year = 1998, - volume = 74, - pages = {2786-2801} -} +@STRING{jpcb = "J. Phys. Chem. B"} -@Article{Cascales98, - author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre}, - title = {Anaesthetic mechanism on a model biological - membrane: A molecular dynamics simulation study}, - journal = {J. Phys. Chem. B}, - year = 1998, - volume = 102, - pages = {625-631} -} +@STRING{mp = "Mol. Phys."} -@Article{Bassolino95, - author = {D. Bassolino and H.~E. Alper and T.~R. Stouch}, - title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID - BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION}, - journal = {J. Am. Chem. Soc.}, - year = 1995, - volume = 117, - pages = {4118-4129} -} +@STRING{pccp = "Phys. Chem. Chem. Phys."} -@Article{Alper95, - author = {H.~E. Alper and T.~R. Stouch}, - title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN - BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS}, - journal = {J. Phys. Chem.}, - year = 1995, - volume = 99, - pages = {5724-5731} -} +@STRING{pnas = "Proc. Natl. Acad. Sci. USA"} -@Article{Sok92, - author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren}, - title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF - SMALL MOLECULES ACROSS A POLYMER MEMBRANE}, - journal = {J. Chem. Phys.}, - year = 1992, - volume = 96, - pages = {4699-4704} -} +@STRING{pra = "Phys. Rev. A"} -@Article{Rabani99, - author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, - title = {Direct Observation of Stretched-Exponential - Relaxation in Low-Temperature Lennard-Jones Systems - Using the Cage Correlation Function}, - journal = prl, - year = {1999}, - volume = 82, - pages = {3649} -} +@STRING{prb = "Phys. Rev. B"} -@Article{Rabani97, - author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, - title = {Calculating the hopping rate for self-diffusion on - rough potential energy surfaces: Cage correlations}, - journal = {J. Chem. Phys.}, - year = 1997, - volume = 107, - pages = {6867-6876} -} +@STRING{pre = "Phys. Rev. E"} -@Article{Gezelter99, - author = {J.~D. Gezelter and E. Rabani and B.~J. Berne}, - title = {Methods for calculating the hopping rate for - orientational and spatial diffusion in a molecular - liquid: $\mbox{CS}_{2}$}, - journal = jcp, - year = 1999, - volume = 110, - pages = 3444 -} +@STRING{prl = "Phys. Rev. Lett."} -@Article{Gezelter98a, - author = {J.~D. Gezelter and E. Rabani and B.~J. Berne}, - title = {Response to 'Comment on a Critique of the - Instantaneous Normal Mode (INM) Approach to - Diffusion'}, - journal = jcp, - year = 1998, - volume = 109, - pages = 4695 -} +@STRING{rmp = "Rev. Mod. Phys."} -@Article{Gezelter97, - author = {J.~D. Gezelter and E. Rabani and B.~J. Berne}, - title = {Can imaginary instantaneous normal mode frequencies - predict barriers to self-diffusion?}, - journal = jcp, - year = 1997, - volume = 107, - pages = 4618 -} -@Article{Zwanzig83, - author = {R. 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Mark}, + Date-Modified = {2006-02-15 10:28:09 -0500}, + Journal = jacs, + Pages = {8638-8639}, + Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers}, + Volume = 123, + Year = 2001} -@Article{Bratko85, - author = {D. Bratko and L. Blum and A. Luzar}, - title = {A simple model for the intermolecular potential of water}, - journal = jcp, - year = 1985, - volume = 83, - number = 12, - pages = {6367-6370} -} +@article{Liu96b, + Author = {Y. Liu and T. Ichiye}, + Date-Modified = {2006-02-15 10:27:07 -0500}, + Journal = jpc, + Pages = {2723-2730}, + Title = {Soft sticky dipole potential for liquid water: a new model}, + Volume = 100, + Year = 1996} -@Article{Bratko95, - author = {L. Blum and F. Vericat and D. Bratko}, - title = {Towards an analytical model of water: The octupolar model}, - journal = jcp, - year = 1995, - volume = 102, - number = 3, - pages = {1461-1462} -} +@article{Liu96a, + Author = {Y. Liu and T. 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Nagle}, + Date-Modified = {2006-02-15 10:21:52 -0500}, + Journal = {Physical Review E}, + Number = 5, + Pages = {5668-5677}, + Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples}, + Volume = 61, + Year = 2000} + +@article{Sengupta00, + Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras}, + Date-Modified = {2006-02-15 10:32:00 -0500}, + Journal = {Europhysics Letters}, + Number = 6, + Pages = {722-728}, + Title = {Novel structural Features of the ripple phase of phospholipids}, + Volume = 49, + Year = 2000} +@article{Venable00, + Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, + Date-Modified = {2006-02-15 10:11:19 -0500}, + Journal = jcp, + Number = 10, + Pages = {4822-4832}, + Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles}, + Volume = 112, + Year = 2000} -@Article{Ercolessi02, - author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, - title = {Bending strain-driven modification of surface resconstructions: Au(111)}, - journal = prb, - year = 2002, - volume = 65, - pages = 241406 -} +@article{Lindahl00, + Author = {E. Lindahl and O. Edholm}, + Date-Modified = {2006-02-15 10:26:05 -0500}, + Journal = {Biophysical Journal}, + Month = {July}, + Pages = {426-433}, + Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, + Volume = 79, + Year = 2000} -@Article{Ercolessi88, - author = {F. Ercolessi and M. Parrinello and E. Tosatti}, - title = {Simulation of Gold in the Glue Model.}, - journal = {Philosophical Magazine A}, - year = 1988, - volume = 58, - pages = {213-226} -} +@article{Saiz02, + Author = {L. Saiz and M. 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Daw}, - title = {Embedded-atom-method functions for the fcc metals -$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, - journal = prb, - year = 1986, - volume = 33, - number = 12, - pages = 7983 -} +@article{Darden93, + Author = {T. Darden and D. York and L. Pedersen}, + Date-Modified = {2006-02-15 10:09:52 -0500}, + Journal = {Journal of Chemical Physics}, + Number = 12, + Pages = {10089-10092}, + Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems}, + Volume = 98, + Year = 1993} -@Article{EAM93, - author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes}, - title = {The embededd-atom method}, - journal = {Mat. Sci. Rep.}, - year = 1993, - volume = 9, - pages = {251-310} -} +@article{Goetz98, + Author = {R. Goetz and R. 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Bratko}, + Journal = jcp, + Number = 3, + Pages = {1461-1462}, + Title = {Towards an analytical model of water: The octupolar model}, + Volume = 102, + Year = 1995} -@Article{sum:2003, - author = {A.~K. Sum and J.~J. de~Pablo}, - title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, - journal = {Biophysical Journal}, - year = 2003, - volume = 85, - pages = {3636-3645} -} +@article{Tan03, + Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye}, + Journal = cpl, + Pages = {646-652}, + Title = {A temperature of maximum density in soft sticky dipole water}, + Volume = 376, + Year = 2003} -@Article{gomez:2003, - author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom}, - title = {Setting up and optimization of membrane protein simulations}, - journal = {Eur. Biophys. J.}, - year = 2002, - volume = 31, - pages = {217-227} -} +@article{Soper86, + Author = {A.~K. Soper and M.~G. Phillips}, + Journal = cp, + Number = 1, + Pages = {47-60}, + Title = {A new determination of the structure of water at 298K}, + Volume = 107, + Year = 1986} +@article{Plimpton95, + Author = {S. Plimpton}, + Date-Modified = {2006-02-15 10:30:31 -0500}, + Journal = {J. Comp. Phys.}, + Pages = {1-19}, + Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, + Volume = 117, + Year = 1995} -@Article{smondyrev:1999, - author = {A.~M. Smondyrev and M.~L. Berkowitz}, - title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, - journal = {Biophysical Journal}, - year = 1999, - volume = 76, - pages = {2472-2478} -} +@article{Tartaglino02, + Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, + Date-Modified = {2006-02-15 10:34:04 -0500}, + Journal = prb, + Pages = 241406, + Title = {Bending strain-driven modification of surface resconstructions: Au(111)}, + Volume = 65, + Year = 2002} -@Article{nina:2002, - author = {M. Nina and T. Simonson}, - title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments}, - journal = {J. Phys. Chem. B}, - year = 2002, - volume = 106, - pages = {3696-3705} -} +@article{Ercolessi88, + Author = {F. Ercolessi and M. Parrinello and E. Tosatti}, + Journal = {Philosophical Magazine A}, + Pages = {213-226}, + Title = {Simulation of Gold in the Glue Model.}, + Volume = 58, + Year = 1988} -@Article{norberg:2000, - author = {J. Norberg and L. Nilsson}, - title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {1537-1553} -} +@article{Finnis84, + Author = {M.~W Finnis and J.~E. Sinclair}, + Journal = {Phil. Mag. A}, + Pages = {45-55}, + Title = {A Simple Empirical N-Body Potential for Transition-Metals}, + Volume = 50, + Year = 1984} -@Article{patra:2003, - author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen}, - title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions}, - journal = {Biophysical Journal}, - year = 2003, - volume = 84, - pages = {3636-3645} -} +@article{Foiles86, + Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw}, + Date-Modified = {2006-02-15 10:17:44 -0500}, + Journal = prb, + Number = 12, + Pages = 7983, + Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, + Volume = 33, + Year = 1986} -@Article{marrink04, - author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, - title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, - journal = {J. Phys. Chem. B}, - year = 2004, - volume = 108, - pages = {750-760} -} +@article{Daw93, + Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes}, + Date-Modified = {2006-02-15 10:16:13 -0500}, + Journal = {Mat. Sci. Rep.}, + Pages = {251-310}, + Title = {The embededd-atom method}, + Volume = 9, + Year = 1993} -@Article{andersen83, - author = {H.~C. Andersen}, - title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, - journal = {Journal of Computational Physics}, - year = 1983, - volume = 52, - pages = {24-34} -} +@article{Johnson89, + Author = {R.~A. Johnson}, + Date-Modified = {2006-02-15 10:21:36 -0500}, + Journal = prb, + Number = 17, + Pages = 12554, + Title = {Alloy models with the embedded-atom method}, + Volume = 39, + Year = 1989} -@Article{hura00, - author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, - title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, - journal = {J. Chem. Phys.}, - year = 2000, - volume = 113, - pages = {9140-9148} -} +@article{Kol97, + Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler}, + Date-Modified = {2006-02-15 10:24:53 -0500}, + Journal = jcp, + Number = 7, + Pages = {2580-2588}, + Title = {A symplectic method for rigid-body molecular simulation}, + Volume = 107, + Year = 1997} +@article{Hoover85, + Author = {W.~G. Hoover}, + Date-Modified = {2006-02-15 10:21:18 -0500}, + Journal = pra, + Pages = 1695, + Title = {Canonical dynamics: Equilibrium phase-space distributions}, + Volume = 31, + Year = 1985} -@Article{ryckaert77, - author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen}, - title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes}, - journal = {Journal of Computational Physics}, - year = 1977, - volume = 23, - pages = {327-341} -} +@article{Roux91, + Author = {B. Roux and M. Karplus}, + Journal = jpc, + Number = 15, + Pages = {4856-4868}, + Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, + Volume = 95, + Year = 1991} +@article{Marrink94, + Author = {S.~J Marrink and H.~J.~C. Berendsen}, + Journal = jpc, + Number = 15, + Pages = {4155-4168}, + Title = {Simulation of water transport through a lipid membrane}, + Volume = 98, + Year = 1994} -@InBook{fowles99:lagrange, - author = {G.~R. Fowles and G.~L. Cassiday}, - title = {Analytical Mechanics}, - chapter = 10, - publisher = {Saunders College Publishing}, - address = {}, - year = 1999, - edition = {6th} -} +@article{Daw89, + Author = {Murray~S. Daw}, + Journal = {Physical Review B}, + Pages = {7441-7452}, + Title = {Model of metallic cohesion: The embedded-atom method}, + Volume = 39, + Year = 1989} -@Article{petrache00, - author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, - title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {3172-3192} -} +@inbook{Voter95b, + Author = {A.~F. Voter}, + Chapter = 4, + Date-Modified = {2006-02-15 10:35:07 -0500}, + Editor = {J.~H. Westbrook and R.~L. Fleischer}, + Pages = 77, + Publisher = {John Wiley and Sons Ltd}, + Title = {Intermetallic Compounds: Principles and Practice}, + Volume = 1, + Year = 1995} -@Article{egberts88, - author = {E. Egberts and H.~J.~C. Berendsen}, - title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail}, - journal = {J. Chem. Phys.}, - year = 1988, - volume = 89, - pages = {3718-3732} -} +@article{Marrink02, + Author = {S.~J. Marrink and D.~P. Teileman}, + Date-Modified = {2006-02-15 10:28:20 -0500}, + Journal = {Biophysical Journal}, + Pages = {2386-2392}, + Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, + Volume = 83, + Year = 2002} -@Article{Holz00, - author = {M. Holz and S.~R. Heil and A. Sacco}, - title = {Temperature-dependent self-diffusion coefficients of - water and six selected molecular liquids for calibration - in accurate $^1${\sc h} {\sc nmr pfg} measurements}, - journal = {Phys. Chem. Chem. Phys.}, - year = 2000, - volume = 2, - pages = {4740-4742}, -} +@article{Sum03, + Author = {A.~K. Sum and J.~J. de~Pablo}, + Date-Modified = {2006-02-15 10:11:01 -0500}, + Journal = {Biophysical Journal}, + Pages = {3636-3645}, + Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, + Volume = 85, + Year = 2003} -@InCollection{zannoni94, - author = {C. Zannoni}, - title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals}, - booktitle = {The Molecular Dynamics of Liquid Crstals}, - pages = {139-169}, - publisher = {Kluwer Academic Publishers}, - year = 1994, - editor = {G.~R. Luckhurst and C.~A. Veracini}, - chapter = 6 -} +@article{Gomez03, + Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom}, + Date-Modified = {2006-02-15 10:17:14 -0500}, + Journal = {Eur. Biophys. J.}, + Pages = {217-227}, + Title = {Setting up and optimization of membrane protein simulations}, + Volume = 31, + Year = 2002} +@article{Smondyrev99, + Author = {A.~M. Smondyrev and M.~L. Berkowitz}, + Date-Modified = {2006-02-15 10:10:29 -0500}, + Journal = {Biophysical Journal}, + Pages = {2472-2478}, + Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, + Volume = 76, + Year = 1999} -@Article{melchionna93, - author = {S. Melchionna and G. Ciccotti and B.~L. Holian}, - title = {Hoover {\sc npt} dynamics for systems varying in shape and size}, - journal = {Molecular Physics}, - year = 1993, - volume = 78, - pages = {533-544} -} +@article{Nina02, + Author = {M. Nina and T. Simonson}, + Date-Modified = {2006-02-15 10:29:27 -0500}, + Journal = {J. Phys. Chem. B}, + Pages = {3696-3705}, + Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments}, + Volume = 106, + Year = 2002} +@article{Norberg00, + Author = {J. Norberg and L. Nilsson}, + Date-Modified = {2006-02-15 10:29:36 -0500}, + Journal = {Biophysical Journal}, + Pages = {1537-1553}, + Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, + Volume = 79, + Year = 2000} +@article{Patra03, + Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen}, + Date-Modified = {2006-02-15 10:29:58 -0500}, + Journal = {Biophysical Journal}, + Pages = {3636-3645}, + Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions}, + Volume = 84, + Year = 2003} -@Article{Fennell04, - author = {C.~J. Fennell and J.~D. Gezelter}, - title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models}, - journal = jcp, - year = 2004, - volume = 120, - number = 19, - pages = {9175-9184} -} +@article{Marrink04, + Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, + Date-Modified = {2006-02-15 10:28:28 -0500}, + Journal = {J. Phys. Chem. B}, + Pages = {750-760}, + Title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, + Volume = 108, + Year = 2004} -@Article{klein01, - author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, - title = {A coarse Grain Model for Phospholipid Simulations}, - journal = {J. Phys. Chem. B}, - year = 2001, - volume = 105, - pages = {4464-4470} -} +@article{Andersen83, + Author = {H.~C. Andersen}, + Date-Modified = {2006-02-15 10:08:20 -0500}, + Journal = {Journal of Computational Physics}, + Pages = {24-34}, + Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, + Volume = 52, + Year = 1983} +@article{Hura00, + Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, + Date-Modified = {2006-02-15 10:21:28 -0500}, + Journal = {J. Chem. Phys.}, + Pages = {9140-9148}, + Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, + Volume = 113, + Year = 2000} -@Article{marrink03:vesicles, - author = {S.~J. Marrink and A.~E. Mark}, - title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles}, - journal = {J. Am. Chem. Soc.}, - year = 2003, - volume = 125, - pages = {15233-15242} -} +@article{Ryckaert77, + Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen}, + Date-Modified = {2006-02-15 10:31:44 -0500}, + Journal = {Journal of Computational Physics}, + Pages = {327-341}, + Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes}, + Volume = 23, + Year = 1977} -@Article{FletcherReeves, - author = {R. Fletcher and C.~M. Reeves}, - title = {Function minimization by conjugate gradients}, - journal = {Comput. J.}, - year = 1964, - volume = 7, - number = 2, - pages = {149-154} -} +@inbook{Fowles99, + Author = {G.~R. Fowles and G.~L. Cassiday}, + Chapter = 10, + Date-Modified = {2006-02-15 10:18:00 -0500}, + Edition = {6th}, + Publisher = {Saunders College Publishing}, + Title = {Analytical Mechanics}, + Year = 1999} -@Article{PolakRibiere, - author = {E. Polak and G. 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