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Revision 2667 by chrisfen, Fri Mar 24 02:39:59 2006 UTC

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3  
4  
5 < %% Created for Chris Fennell at 2006-03-15 21:43:19 -0500
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6  
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45   @STRING{rmp = "Rev. Mod. Phys."}
46  
47  
48 < @article{Barker73,
49 <        Author = {J.~A. Barker and R.~O. Watts },
50 <        Date-Added = {2006-03-15 18:58:17 -0500},
51 <        Date-Modified = {2006-03-15 21:17:31 -0500},
48 > @article{Kolafa92,
49 >        Author = {J. Kolafa and J.~W. Perram},
50 >        Date-Added = {2006-03-21 09:41:58 -0500},
51 >        Date-Modified = {2006-03-21 09:42:47 -0500},
52 >        Journal = {Mol. Simul.},
53 >        Pages = {351-368},
54 >        Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
55 >        Volume = {9},
56 >        Year = {1992}}
57 >
58 > @article{Karasawa89,
59 >        Author = {N. Karasawa and W.~A. {Goddard III}},
60 >        Date-Added = {2006-03-21 09:11:44 -0500},
61 >        Date-Modified = {2006-03-21 09:13:00 -0500},
62 >        Journal = {J. Phys. Chem.},
63 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
64 >        Pages = {7320-7327},
65 >        Title = {Acceleration of Convergence for Lattice Sums},
66 >        Volume = {93},
67 >        Year = {1989}}
68 >
69 > @article{Roux99,
70 >        Author = {B. Roux and T. Simonson},
71 >        Date-Added = {2006-03-19 20:10:18 -0500},
72 >        Date-Modified = {2006-03-19 20:12:10 -0500},
73 >        Journal = {Biophys. Chem.},
74 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
75 >        Pages = {1-20},
76 >        Title = {Implicit solvent models},
77 >        Volume = {78},
78 >        Year = {1999}}
79 >
80 > @article{Rokhlin85,
81 >        Author = {V. Rokhlin},
82 >        Date-Added = {2006-03-19 20:02:25 -0500},
83 >        Date-Modified = {2006-03-19 20:04:19 -0500},
84 >        Doi = {10.1016/0021-9991(85)90002-6},
85 >        Journal = {J. Comput. Phys.},
86 >        Month = {September},
87 >        Number = {2},
88 >        Pages = {187-207},
89 >        Title = {Rapid solution of integral equations of classical potential theory},
90 >        Volume = {60},
91 >        Year = {1985}}
92 >
93 > @article{Grossfield00,
94 >        Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
95 >        Date-Added = {2006-03-19 19:52:19 -0500},
96 >        Date-Modified = {2006-03-19 19:54:14 -0500},
97 >        Journal = {Proteins},
98 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
99 >        Pages = {211-223},
100 >        Title = {Dipole Lattice Membrane Model for Protein Calculations},
101 >        Volume = {41},
102 >        Year = {2000}}
103 >
104 > @article{Born20,
105 >        Author = {M. Born},
106 >        Date-Added = {2006-03-19 18:05:01 -0500},
107 >        Date-Modified = {2006-03-19 18:07:42 -0500},
108 >        Journal = {Z. Physik},
109 >        Pages = {45-48},
110 >        Title = {Volumen und hydratationswame der ionen},
111 >        Volume = {1},
112 >        Year = {1920}}
113 >
114 > @article{Luty96,
115 >        Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
116 >        Date-Added = {2006-03-18 20:59:19 -0500},
117 >        Date-Modified = {2006-03-18 21:00:33 -0500},
118 >        Journal = {J. Phys. Chem.},
119 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
120 >        Number = {7},
121 >        Pages = {2581-2587},
122 >        Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
123 >        Volume = {100},
124 >        Year = {1996}}
125 >
126 > @article{Rhee89,
127 >        Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
128 >        Date-Added = {2006-03-18 20:48:07 -0500},
129 >        Date-Modified = {2006-03-18 20:51:09 -0500},
130 >        Journal = {Phys. Rev. B},
131 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
132 >        Number = {1},
133 >        Pages = {36-42},
134 >        Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
135 >        Volume = {40},
136 >        Year = {1989}}
137 >
138 > @article{Hunenberger99a,
139 >        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
140 >        Date-Added = {2006-03-18 20:14:24 -0500},
141 >        Date-Modified = {2006-03-18 20:16:01 -0500},
142 >        Journal = {J. Chem. Phys.},
143 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
144 >        Number = {4},
145 >        Pages = {1856-1872},
146 >        Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
147 >        Volume = {110},
148 >        Year = {1999}}
149 >
150 > @article{Roberts95,
151 >        Author = {J.~E. Roberts and J. Schnitker},
152 >        Date-Added = {2006-03-18 20:12:23 -0500},
153 >        Date-Modified = {2006-03-18 20:13:36 -0500},
154 >        Journal = {J. Phys. Chem.},
155 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
156 >        Pages = {1322-1331},
157 >        Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
158 >        Volume = {99},
159 >        Year = {1995}}
160 >
161 > @article{Roberts94,
162 >        Author = {J.~E. Roberts and J. Schnitker},
163 >        Date-Added = {2006-03-18 20:10:37 -0500},
164 >        Date-Modified = {2006-03-18 20:12:19 -0500},
165 >        Journal = {J. Chem. Phys.},
166 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
167 >        Number = {6},
168 >        Pages = {5024-5031},
169 >        Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
170 >        Volume = {101},
171 >        Year = {1994}}
172 >
173 > @article{Yeh99,
174 >        Author = {I.-C. Yeh and M.~L. Berkowitz},
175 >        Date-Added = {2006-03-18 19:24:27 -0500},
176 >        Date-Modified = {2006-03-18 19:26:08 -0500},
177 >        Journal = {J. Chem. Phys.},
178 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
179 >        Number = {7},
180 >        Pages = {3155-3162},
181 >        Title = {Ewald summation for systems with slab geometry},
182 >        Volume = {111},
183 >        Year = {1999}}
184 >
185 > @article{Parry76,
186 >        Author = {D.~E. Parry},
187 >        Date-Added = {2006-03-18 19:11:01 -0500},
188 >        Date-Modified = {2006-03-18 19:14:01 -0500},
189 >        Journal = {Surf. Sci.},
190 >        Pages = {195},
191 >        Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
192 >        Volume = {54},
193 >        Year = {1976}}
194 >
195 > @article{Parry75,
196 >        Author = {D.~E. Parry},
197 >        Date-Added = {2006-03-18 19:08:40 -0500},
198 >        Date-Modified = {2006-03-18 19:16:14 -0500},
199 >        Journal = {Surf. Sci.},
200 >        Pages = {433-440},
201 >        Title = {The electrostatic potential in the surface region of an ionic crystal},
202 >        Volume = {49},
203 >        Year = {1975}}
204 >
205 > @article{deLeeuw79,
206 >        Author = {S.~W. {de Leeuw} and J.~W. Perram},
207 >        Date-Added = {2006-03-18 19:05:18 -0500},
208 >        Date-Modified = {2006-03-18 19:07:48 -0500},
209          Journal = {Mol. Phys.},
210 <        Pages = {789=792},
210 >        Pages = {1313-1327},
211 >        Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
212 >        Volume = {37},
213 >        Year = {1979}}
214 >
215 > @article{Heyes77,
216 >        Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
217 >        Date-Added = {2006-03-18 19:02:16 -0500},
218 >        Date-Modified = {2006-03-18 19:04:48 -0500},
219 >        Journal = {J. Chem. Soc., Faraday Trans. II},
220 >        Number = {7},
221 >        Pages = {1485-1496},
222 >        Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
223 >        Volume = {73},
224 >        Year = {1977}}
225 >
226 > @article{Spohr97,
227 >        Author = {E. Spohr},
228 >        Date-Added = {2006-03-18 18:51:02 -0500},
229 >        Date-Modified = {2006-03-18 18:52:21 -0500},
230 >        Journal = {J. Chem. Phys.},
231 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
232 >        Number = {16},
233 >        Pages = {6342-6348},
234 >        Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
235 >        Volume = {107},
236 >        Year = {1997}}
237 >
238 > @article{York94,
239 >        Author = {D. York and W. Yang},
240 >        Date-Added = {2006-03-18 11:52:58 -0500},
241 >        Date-Modified = {2006-03-18 11:54:19 -0500},
242 >        Journal = {J. Chem. Phys.},
243 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
244 >        Number = {4},
245 >        Pages = {3298-3300},
246 >        Title = {The fast Fourier Poisson method for calculating Ewald sums},
247 >        Volume = {101},
248 >        Year = {1994}}
249 >
250 > @article{Shimada93,
251 >        Author = {J. Shimada and H. Kaneko and T. Takada},
252 >        Date-Added = {2006-03-18 11:10:38 -0500},
253 >        Date-Modified = {2006-03-18 11:12:10 -0500},
254 >        Journal = {J. Comp. Chem.},
255 >        Pages = {867-78},
256 >        Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
257 >        Volume = {14},
258 >        Year = {1993}}
259 >
260 > @article{Luty94,
261 >        Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
262 >        Date-Added = {2006-03-18 10:37:17 -0500},
263 >        Date-Modified = {2006-03-18 11:09:55 -0500},
264 >        Journal = {Mol. Simul.},
265 >        Pages = {11-20},
266 >        Title = {A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems},
267 >        Volume = {14},
268 >        Year = {1994}}
269 >
270 > @book{Hockney81,
271 >        Address = {New York},
272 >        Author = {R.~W. Hockney and J.~W. Eastwood},
273 >        Date-Added = {2006-03-18 10:33:19 -0500},
274 >        Date-Modified = {2006-03-18 10:35:04 -0500},
275 >        Publisher = {McGraw-Hill},
276 >        Title = {Computer Simulation Using Particles},
277 >        Year = {1981}}
278 >
279 > @article{Sagui99,
280 >        Author = {C. Sagui and T.~A. Darden},
281 >        Date-Added = {2006-03-17 18:27:01 -0500},
282 >        Date-Modified = {2006-03-23 13:48:12 -0500},
283 >        Journal = {Annu. Rev. Biophys. Biomol. Struct.},
284 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_electrostaticInBiomolecules_99.pdf},
285 >        Pages = {155-179},
286 >        Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
287 >        Volume = {28},
288 >        Year = {1999}}
289 >
290 > @article{Perram88,
291 >        Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
292 >        Date-Added = {2006-03-17 13:42:04 -0500},
293 >        Date-Modified = {2006-03-17 13:59:01 -0500},
294 >        Journal = {Mol. Phys.},
295 >        Pages = {875-893},
296 >        Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
297 >        Volume = {65},
298 >        Year = {1988}}
299 >
300 > @article{Woodcock71,
301 >        Author = {L.~V. Woodcock and K. Singer},
302 >        Date-Added = {2006-03-17 11:14:17 -0500},
303 >        Date-Modified = {2006-03-17 11:16:52 -0500},
304 >        Journal = {Trans. Faraday Soc.},
305 >        Pages = {12-30},
306 >        Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
307 >        Volume = {67},
308 >        Year = {1971}}
309 >
310 > @article{Smith81,
311 >        Author = {E.~R. Smith},
312 >        Date-Added = {2006-03-16 13:47:17 -0500},
313 >        Date-Modified = {2006-03-16 13:48:34 -0500},
314 >        Journal = {Proc. R. Soc. London Ser. A},
315 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
316 >        Pages = {475-505},
317 >        Title = {Electrostatic Energy in Ionic Crystals},
318 >        Volume = {375},
319 >        Year = {1981}}
320 >
321 > @article{Weber00,
322 >        Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
323 >        Date-Added = {2006-03-16 09:49:22 -0500},
324 >        Date-Modified = {2006-03-16 09:51:17 -0500},
325 >        Doi = {10.1021/jp9937757},
326 >        Journal = {J. Phys. Chem. B},
327 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
328 >        Number = {15},
329 >        Pages = {3668-3675},
330 >        Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
331 >        Volume = {104},
332 >        Year = {2000}}
333 >
334 > @article{Hunenberger99b,
335 >        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
336 >        Date-Added = {2006-03-16 09:45:10 -0500},
337 >        Date-Modified = {2006-03-18 20:16:16 -0500},
338 >        Journal = {Biophys. Chem.},
339 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
340 >        Pages = {69-88},
341 >        Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
342 >        Volume = {78},
343 >        Year = {1999}}
344 >
345 > @article{Petersen95,
346 >        Author = {H.~G. Petersen},
347 >        Date-Added = {2006-03-16 08:43:02 -0500},
348 >        Date-Modified = {2006-03-16 08:44:32 -0500},
349 >        Journal = {J. Chem. Phys.},
350 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
351 >        Month = {September},
352 >        Number = {9},
353 >        Pages = {3668-3679},
354 >        Title = {Accuracy and efficiency of the particle mesh Ewald method},
355 >        Volume = {103},
356 >        Year = {1995}}
357 >
358 > @article{Luty95,
359 >        Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
360 >        Date-Added = {2006-03-16 08:39:13 -0500},
361 >        Date-Modified = {2006-03-16 08:41:15 -0500},
362 >        Journal = {J. Chem. Phys.},
363 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
364 >        Number = {8},
365 >        Pages = {3014-3021},
366 >        Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
367 >        Volume = {103},
368 >        Year = {1995}}
369 >
370 > @article{Barker73,
371 >        Author = {J.~A. Barker and R.~O. Watts},
372 >        Date-Added = {2006-03-15 18:58:17 -0500},
373 >        Date-Modified = {2006-03-18 11:36:56 -0500},
374 >        Journal = {Mol. Phys.},
375 >        Pages = {789-792},
376          Title = {Monte Carlo studies of the dielectric properties of water-like models},
377          Volume = {26},
378          Year = {1973}}
# Line 107 | Line 429
429   @article{Ewald21,
430          Author = {P.~P. Ewald},
431          Date-Added = {2006-03-13 13:32:04 -0500},
432 <        Date-Modified = {2006-03-13 13:32:55 -0500},
432 >        Date-Modified = {2006-03-16 22:39:27 -0500},
433          Journal = {Ann. Physik},
434 <        Pages = {253},
434 >        Pages = {253-287},
435 >        Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
436          Volume = {64},
437          Year = {1921}}
438  
# Line 165 | Line 488
488   @article{Essmann95,
489          Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
490          Date-Added = {2006-03-05 12:25:25 -0500},
491 <        Date-Modified = {2006-03-05 12:29:07 -0500},
491 >        Date-Modified = {2006-03-23 13:47:48 -0500},
492          Journal = {J. Chem. Phys.},
493 <        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
493 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
494          Number = {19},
495          Pages = {8577-8593},
496          Title = {A smooth particle mesh Ewald method},
# Line 1549 | Line 1872
1872  
1873   @article{Darden93,
1874          Author = {T. Darden and D. York and L. Pedersen},
1875 <        Date-Modified = {2006-02-15 10:09:52 -0500},
1875 >        Date-Modified = {2006-03-16 08:37:25 -0500},
1876          Journal = {Journal of Chemical Physics},
1877 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
1878          Number = 12,
1879          Pages = {10089-10092},
1880          Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
# Line 1958 | Line 2282
2282  
2283   @article{Marrink03,
2284          Author = {S.~J. Marrink and A.~E. Mark},
2285 <        Date-Modified = {2006-02-15 10:28:41 -0500},
2285 >        Date-Modified = {2006-03-16 09:54:52 -0500},
2286          Journal = {J. Am. Chem. Soc.},
2287          Pages = {15233-15242},
2288 <        Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2288 >        Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2289          Volume = 125,
2290          Year = 2003}
2291  

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