--- trunk/electrostaticMethodsPaper/electrostaticMethods.bib	2006/02/20 12:32:54	2595
+++ trunk/electrostaticMethodsPaper/electrostaticMethods.bib	2006/03/19 02:48:19	2637
@@ -2,7 +2,7 @@
 %% http://bibdesk.sourceforge.net/
 
 
-%% Created for Chris Fennell at 2006-02-18 16:51:35 -0500 
+%% Created for Chris Fennell at 2006-03-18 21:00:37 -0500 
 
 
 %% Saved with string encoding Western (ASCII) 
@@ -43,8 +43,394 @@
 @STRING{prl = "Phys. Rev. Lett."}
 
 @STRING{rmp = "Rev. Mod. Phys."}
+
+
+@article{Luty96,
+	Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
+	Date-Added = {2006-03-18 20:59:19 -0500},
+	Date-Modified = {2006-03-18 21:00:33 -0500},
+	Journal = {J. Phys. Chem.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
+	Number = {7},
+	Pages = {2581-2587},
+	Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
+	Volume = {100},
+	Year = {1996}}
+
+@article{Rhee89,
+	Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
+	Date-Added = {2006-03-18 20:48:07 -0500},
+	Date-Modified = {2006-03-18 20:51:09 -0500},
+	Journal = {Phys. Rev. B},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
+	Number = {1},
+	Pages = {36-42},
+	Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
+	Volume = {40},
+	Year = {1989}}
+
+@article{Hunenberger99a,
+	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
+	Date-Added = {2006-03-18 20:14:24 -0500},
+	Date-Modified = {2006-03-18 20:16:01 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
+	Number = {4},
+	Pages = {1856-1872},
+	Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
+	Volume = {110},
+	Year = {1999}}
+
+@article{Roberts95,
+	Author = {J.~E. Roberts and J. Schnitker},
+	Date-Added = {2006-03-18 20:12:23 -0500},
+	Date-Modified = {2006-03-18 20:13:36 -0500},
+	Journal = {J. Phys. Chem.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
+	Pages = {1322-1331},
+	Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
+	Volume = {99},
+	Year = {1995}}
+
+@article{Roberts94,
+	Author = {J.~E. Roberts and J. Schnitker},
+	Date-Added = {2006-03-18 20:10:37 -0500},
+	Date-Modified = {2006-03-18 20:12:19 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
+	Number = {6},
+	Pages = {5024-5031},
+	Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
+	Volume = {101},
+	Year = {1994}}
+
+@article{Yeh99,
+	Author = {I.-C. Yeh and M.~L. Berkowitz},
+	Date-Added = {2006-03-18 19:24:27 -0500},
+	Date-Modified = {2006-03-18 19:26:08 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
+	Number = {7},
+	Pages = {3155-3162},
+	Title = {Ewald summation for systems with slab geometry},
+	Volume = {111},
+	Year = {1999}}
+
+@article{Parry76,
+	Author = {D.~E. Parry},
+	Date-Added = {2006-03-18 19:11:01 -0500},
+	Date-Modified = {2006-03-18 19:14:01 -0500},
+	Journal = {Surf. Sci.},
+	Pages = {195},
+	Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
+	Volume = {54},
+	Year = {1976}}
+
+@article{Parry75,
+	Author = {D.~E. Parry},
+	Date-Added = {2006-03-18 19:08:40 -0500},
+	Date-Modified = {2006-03-18 19:16:14 -0500},
+	Journal = {Surf. Sci.},
+	Pages = {433-440},
+	Title = {The electrostatic potential in the surface region of an ionic crystal},
+	Volume = {49},
+	Year = {1975}}
+
+@article{deLeeuw79,
+	Author = {S.~W. {de Leeuw} and J.~W. Perram},
+	Date-Added = {2006-03-18 19:05:18 -0500},
+	Date-Modified = {2006-03-18 19:07:48 -0500},
+	Journal = {Mol. Phys.},
+	Pages = {1313-1327},
+	Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
+	Volume = {37},
+	Year = {1979}}
+
+@article{Heyes77,
+	Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
+	Date-Added = {2006-03-18 19:02:16 -0500},
+	Date-Modified = {2006-03-18 19:04:48 -0500},
+	Journal = {J. Chem. Soc., Faraday Trans. II},
+	Number = {7},
+	Pages = {1485-1496},
+	Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
+	Volume = {73},
+	Year = {1977}}
+
+@article{Spohr97,
+	Author = {E. Spohr},
+	Date-Added = {2006-03-18 18:51:02 -0500},
+	Date-Modified = {2006-03-18 18:52:21 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
+	Number = {16},
+	Pages = {6342-6348},
+	Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
+	Volume = {107},
+	Year = {1997}}
+
+@article{York94,
+	Author = {D. York and W. Yang},
+	Date-Added = {2006-03-18 11:52:58 -0500},
+	Date-Modified = {2006-03-18 11:54:19 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
+	Number = {4},
+	Pages = {3298-3300},
+	Title = {The fast Fourier Poisson method for calculating Ewald sums},
+	Volume = {101},
+	Year = {1994}}
+
+@article{Shimada93,
+	Author = {J. Shimada and H. Kaneko and T. Takada},
+	Date-Added = {2006-03-18 11:10:38 -0500},
+	Date-Modified = {2006-03-18 11:12:10 -0500},
+	Journal = {J. Comp. Chem.},
+	Pages = {867-78},
+	Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
+	Volume = {14},
+	Year = {1993}}
+
+@article{Luty94,
+	Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
+	Date-Added = {2006-03-18 10:37:17 -0500},
+	Date-Modified = {2006-03-18 11:09:55 -0500},
+	Journal = {Mol. Simul.},
+	Pages = {11-20},
+	Title = {A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems},
+	Volume = {14},
+	Year = {1994}}
+
+@book{Hockney81,
+	Address = {New York},
+	Author = {R.~W. Hockney and J.~W. Eastwood},
+	Date-Added = {2006-03-18 10:33:19 -0500},
+	Date-Modified = {2006-03-18 10:35:04 -0500},
+	Publisher = {McGraw-Hill},
+	Title = {Computer Simulation Using Particles},
+	Year = {1981}}
+
+@article{Sagui99,
+	Author = {C. Sagui and T.~A. Darden},
+	Date-Added = {2006-03-17 18:27:01 -0500},
+	Date-Modified = {2006-03-17 18:29:36 -0500},
+	Journal = {Annu. Rev. Biophys. Biomol. Struct.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Darden_electrostaticInBiomolecules_99.pdf},
+	Pages = {155-179},
+	Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
+	Volume = {28},
+	Year = {1999}}
+
+@article{Perram88,
+	Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
+	Date-Added = {2006-03-17 13:42:04 -0500},
+	Date-Modified = {2006-03-17 13:59:01 -0500},
+	Journal = {Mol. Phys.},
+	Pages = {875-893},
+	Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
+	Volume = {65},
+	Year = {1988}}
+
+@article{Woodcock71,
+	Author = {L.~V. Woodcock and K. Singer},
+	Date-Added = {2006-03-17 11:14:17 -0500},
+	Date-Modified = {2006-03-17 11:16:52 -0500},
+	Journal = {Trans. Faraday Soc.},
+	Pages = {12-30},
+	Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
+	Volume = {67},
+	Year = {1971}}
+
+@article{Smith81,
+	Author = {E.~R. Smith},
+	Date-Added = {2006-03-16 13:47:17 -0500},
+	Date-Modified = {2006-03-16 13:48:34 -0500},
+	Journal = {Proc. R. Soc. London Ser. A},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
+	Pages = {475-505},
+	Title = {Electrostatic Energy in Ionic Crystals},
+	Volume = {375},
+	Year = {1981}}
+
+@article{Weber00,
+	Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
+	Date-Added = {2006-03-16 09:49:22 -0500},
+	Date-Modified = {2006-03-16 09:51:17 -0500},
+	Doi = {10.1021/jp9937757},
+	Journal = {J. Phys. Chem. B},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
+	Number = {15},
+	Pages = {3668-3675},
+	Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
+	Volume = {104},
+	Year = {2000}}
+
+@article{Hunenberger99b,
+	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
+	Date-Added = {2006-03-16 09:45:10 -0500},
+	Date-Modified = {2006-03-18 20:16:16 -0500},
+	Journal = {Biophys. Chem.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
+	Pages = {69-88},
+	Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
+	Volume = {78},
+	Year = {1999}}
+
+@article{Petersen95,
+	Author = {H.~G. Petersen},
+	Date-Added = {2006-03-16 08:43:02 -0500},
+	Date-Modified = {2006-03-16 08:44:32 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
+	Month = {September},
+	Number = {9},
+	Pages = {3668-3679},
+	Title = {Accuracy and efficiency of the particle mesh Ewald method},
+	Volume = {103},
+	Year = {1995}}
+
+@article{Luty95,
+	Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
+	Date-Added = {2006-03-16 08:39:13 -0500},
+	Date-Modified = {2006-03-16 08:41:15 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
+	Number = {8},
+	Pages = {3014-3021},
+	Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
+	Volume = {103},
+	Year = {1995}}
+
+@article{Barker73,
+	Author = {J.~A. Barker and R.~O. Watts },
+	Date-Added = {2006-03-15 18:58:17 -0500},
+	Date-Modified = {2006-03-18 11:36:56 -0500},
+	Journal = {Mol. Phys.},
+	Pages = {789-792},
+	Title = {Monte Carlo studies of the dielectric properties of water-like models},
+	Volume = {26},
+	Year = {1973}}
+
+@article{Adams79,
+	Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
+	Date-Added = {2006-03-15 17:46:36 -0500},
+	Date-Modified = {2006-03-15 17:48:04 -0500},
+	Journal = {Mol. Phys.},
+	Number = {2},
+	Pages = {387-400},
+	Title = {The computer simulation of polar liquids},
+	Volume = {38},
+	Year = {1979}}
+
+@article{Rahman71,
+	Author = {A. Rahman and F.~H. Stillinger},
+	Date-Added = {2006-03-15 17:04:53 -0500},
+	Date-Modified = {2006-03-15 17:07:29 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
+	Month = {October},
+	Number = {7},
+	Pages = {3336-3359},
+	Title = {Molecular Dynamics Study of Liquid Water},
+	Volume = {55},
+	Year = {1971}}
+
+@article{Andrea83,
+	Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
+	Date-Added = {2006-03-15 15:16:12 -0500},
+	Date-Modified = {2006-03-15 15:18:10 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
+	Number = {9},
+	Pages = {4576-4584},
+	Title = {The role of long ranged forces in determining the structure and properties of liquid water},
+	Volume = {79},
+	Year = {1983}}
+
+@article{Brush66,
+	Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
+	Date-Added = {2006-03-13 16:55:39 -0500},
+	Date-Modified = {2006-03-13 17:01:15 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
+	Month = {September},
+	Number = {6},
+	Pages = {2102-2118},
+	Title = {Monte Carlo Study of a One-Component Plasma. I},
+	Volume = {45},
+	Year = {1966}}
 
+@article{Ewald21,
+	Author = {P.~P. Ewald},
+	Date-Added = {2006-03-13 13:32:04 -0500},
+	Date-Modified = {2006-03-16 22:39:27 -0500},
+	Journal = {Ann. Physik},
+	Pages = {253-287},
+	Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
+	Volume = {64},
+	Year = {1921}}
 
+@article{Jones56,
+	Author = {R.~E. Jones and D.~H. Templeton},
+	Date-Added = {2006-03-13 13:25:58 -0500},
+	Date-Modified = {2006-03-13 13:27:15 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
+	Number = {5},
+	Pages = {1062-1063},
+	Title = {Optimum Atomic Shape for Bertaut Series},
+	Volume = {25},
+	Year = {1956}}
+
+@article{Heyes81,
+	Author = {D.~M. Heyes},
+	Date-Added = {2006-03-13 13:12:45 -0500},
+	Date-Modified = {2006-03-13 13:14:27 -0500},
+	Journal = {J. Chem. Phys.},
+	Keywords = {Empty Keywords},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
+	Number = {3},
+	Pages = {1924-1929},
+	Title = {Electrostatic potentials and fields in infinite point charge lattices},
+	Volume = {74},
+	Year = {1981}}
+
+@article{Steinbach94,
+	Author = {P.~J. Steinbach and B.~R. Brooks},
+	Date-Added = {2006-03-12 19:26:45 -0500},
+	Date-Modified = {2006-03-12 19:29:43 -0500},
+	Doi = {10.1002/jcc.540150702},
+	Journal = {J. Comput. Chem.},
+	Number = {7},
+	Pages = {667-683},
+	Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
+	Volume = {15},
+	Year = {1994}}
+
+@article{deLeeuw80,
+	Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
+	Date-Added = {2006-03-07 10:26:31 -0500},
+	Date-Modified = {2006-03-07 10:30:11 -0500},
+	Journal = {Proc. R. Soc. London Ser. A},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
+	Number = {1752},
+	Pages = {27-56},
+	Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
+	Volume = {373},
+	Year = {1980}}
+
+@article{Essmann95,
+	Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
+	Date-Added = {2006-03-05 12:25:25 -0500},
+	Date-Modified = {2006-03-05 12:29:07 -0500},
+	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
+	Number = {19},
+	Pages = {8577-8593},
+	Title = {A smooth particle mesh Ewald method},
+	Volume = {103},
+	Year = {1995}}
+
 @article{Kast03,
 	Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
 	Date-Added = {2006-02-18 16:47:26 -0500},
@@ -1420,8 +1806,9 @@
 
 @article{Darden93,
 	Author = {T. Darden and D. York and L. Pedersen},
-	Date-Modified = {2006-02-15 10:09:52 -0500},
+	Date-Modified = {2006-03-16 08:37:25 -0500},
 	Journal = {Journal of Chemical Physics},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
 	Number = 12,
 	Pages = {10089-10092},
 	Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
@@ -1458,8 +1845,9 @@
 
 @article{Metropolis53,
 	Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
-	Date-Modified = {2006-02-15 10:29:14 -0500},
+	Date-Modified = {2006-03-09 10:44:24 -0500},
 	Journal = {J. Chem. Phys.},
+	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
 	Pages = {1087-1092},
 	Title = {Equation of State Calculations by Fast Computing Machines},
 	Volume = 21,
@@ -1828,10 +2216,10 @@
 
 @article{Marrink03,
 	Author = {S.~J. Marrink and A.~E. Mark},
-	Date-Modified = {2006-02-15 10:28:41 -0500},
+	Date-Modified = {2006-03-16 09:54:52 -0500},
 	Journal = {J. Am. Chem. Soc.},
 	Pages = {15233-15242},
-	Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
+	Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
 	Volume = 125,
 	Year = 2003}
 
@@ -1977,8 +2365,8 @@
 	Year = 2000}
 
 @article{Meineke05,
-	Author = {M.~A. Meineke and C.~F. Vardeman~II and T. Lin and C.~J. Fennell and J.~D. Gezelter},
-	Date-Modified = {2006-02-15 09:09:23 -0500},
+	Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
+	Date-Modified = {2006-03-05 12:37:31 -0500},
 	Journal = {J. Comp. Chem.},
 	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
 	Pages = {252-271},
@@ -2144,8 +2532,8 @@
 	Year = 1975}
 
 @article{Spoel98,
-	Author = {D. van der Spoel and P.~J. van Maaren and H.~J.~C. Berendsen},
-	Date-Modified = {2006-02-15 10:33:13 -0500},
+	Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
+	Date-Modified = {2006-03-05 12:38:54 -0500},
 	Journal = jcp,
 	Number = 24,
 	Pages = {10220-10230},