--- trunk/electrostaticMethodsPaper/electrostaticMethods.bib 2006/03/11 18:05:50 2609 +++ trunk/electrostaticMethodsPaper/electrostaticMethods.bib 2006/03/16 15:03:20 2630 @@ -2,7 +2,7 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Chris Fennell at 2006-03-11 12:19:21 -0500 +%% Created for Chris Fennell at 2006-03-16 10:02:01 -0500 %% Saved with string encoding Western (ASCII) @@ -45,6 +45,160 @@ @STRING{rmp = "Rev. Mod. Phys."} +@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{Hunenberger99, + Author = {P.~H. H\"{u}nenberger and J.~A. McCammon}, + Date-Added = {2006-03-16 09:45:10 -0500}, + Date-Modified = {2006-03-16 09:49:15 -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 = {2006-03-15 21:17:31 -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 = {2006-03-13 13:32:55 -0500}, + Journal = {Ann. Physik}, + Pages = {253}, + 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}, @@ -65,7 +219,7 @@ 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 }, + Title = {A smooth particle mesh Ewald method}, Volume = {103}, Year = {1995}} @@ -1444,8 +1598,9 @@ @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}, @@ -1853,10 +2008,10 @@ @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}