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root/group/trunk/electrostaticMethodsPaper/electrostaticMethods.bib
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# User Rev Content
1 chrisfen 2594 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3 chrisfen 2575
4    
5 chrisfen 2649 %% Created for Chris Fennell at 2006-03-21 09:57:21 -0500
6 chrisfen 2575
7    
8 chrisfen 2594 %% Saved with string encoding Western (ASCII)
9 chrisfen 2575
10    
11 chrisfen 2594 @STRING{acp = "Adv. Chem. Phys."}
12 chrisfen 2575
13 chrisfen 2594 @STRING{cp = "Chem. Phys."}
14 chrisfen 2575
15 chrisfen 2594 @STRING{cpl = "Chem. Phys. Lett."}
16 chrisfen 2575
17 chrisfen 2594 @STRING{jacs = "J. Am. Chem. Soc."}
18 chrisfen 2575
19 chrisfen 2594 @STRING{jcc = "J. Comput. Chem."}
20 chrisfen 2575
21 chrisfen 2594 @STRING{jcp = "J. Chem. Phys."}
22 chrisfen 2575
23 chrisfen 2594 @STRING{jml = "J. Mol. Liq."}
24 chrisfen 2575
25 chrisfen 2594 @STRING{jpc = "J. Phys. Chem."}
26 chrisfen 2575
27 chrisfen 2594 @STRING{jpca = "J. Phys. Chem. A"}
28 chrisfen 2575
29 chrisfen 2594 @STRING{jpcb = "J. Phys. Chem. B"}
30 chrisfen 2575
31 chrisfen 2594 @STRING{mp = "Mol. Phys."}
32 chrisfen 2575
33 chrisfen 2594 @STRING{pccp = "Phys. Chem. Chem. Phys."}
34 chrisfen 2575
35 chrisfen 2594 @STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36 chrisfen 2575
37 chrisfen 2594 @STRING{pra = "Phys. Rev. A"}
38 chrisfen 2575
39 chrisfen 2594 @STRING{prb = "Phys. Rev. B"}
40 chrisfen 2575
41 chrisfen 2594 @STRING{pre = "Phys. Rev. E"}
42 chrisfen 2575
43 chrisfen 2594 @STRING{prl = "Phys. Rev. Lett."}
44 chrisfen 2575
45 chrisfen 2594 @STRING{rmp = "Rev. Mod. Phys."}
46 chrisfen 2575
47    
48 chrisfen 2649 @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 chrisfen 2639 @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 chrisfen 2637 @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 = {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 chrisfen 2636 @article{Sagui99,
280     Author = {C. Sagui and T.~A. Darden},
281     Date-Added = {2006-03-17 18:27:01 -0500},
282     Date-Modified = {2006-03-17 18:29:36 -0500},
283     Journal = {Annu. Rev. Biophys. Biomol. Struct.},
284     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/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 chrisfen 2630 @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 chrisfen 2637 @article{Hunenberger99b,
335 chrisfen 2630 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
336     Date-Added = {2006-03-16 09:45:10 -0500},
337 chrisfen 2637 Date-Modified = {2006-03-18 20:16:16 -0500},
338 chrisfen 2630 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 chrisfen 2629 @article{Barker73,
371     Author = {J.~A. Barker and R.~O. Watts },
372     Date-Added = {2006-03-15 18:58:17 -0500},
373 chrisfen 2637 Date-Modified = {2006-03-18 11:36:56 -0500},
374 chrisfen 2629 Journal = {Mol. Phys.},
375 chrisfen 2637 Pages = {789-792},
376 chrisfen 2629 Title = {Monte Carlo studies of the dielectric properties of water-like models},
377     Volume = {26},
378     Year = {1973}}
379    
380     @article{Adams79,
381     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
382     Date-Added = {2006-03-15 17:46:36 -0500},
383     Date-Modified = {2006-03-15 17:48:04 -0500},
384     Journal = {Mol. Phys.},
385     Number = {2},
386     Pages = {387-400},
387     Title = {The computer simulation of polar liquids},
388     Volume = {38},
389     Year = {1979}}
390    
391     @article{Rahman71,
392     Author = {A. Rahman and F.~H. Stillinger},
393     Date-Added = {2006-03-15 17:04:53 -0500},
394     Date-Modified = {2006-03-15 17:07:29 -0500},
395     Journal = {J. Chem. Phys.},
396     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
397     Month = {October},
398     Number = {7},
399     Pages = {3336-3359},
400     Title = {Molecular Dynamics Study of Liquid Water},
401     Volume = {55},
402     Year = {1971}}
403    
404     @article{Andrea83,
405     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
406     Date-Added = {2006-03-15 15:16:12 -0500},
407     Date-Modified = {2006-03-15 15:18:10 -0500},
408     Journal = {J. Chem. Phys.},
409     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
410     Number = {9},
411     Pages = {4576-4584},
412     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
413     Volume = {79},
414     Year = {1983}}
415    
416 chrisfen 2612 @article{Brush66,
417     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
418     Date-Added = {2006-03-13 16:55:39 -0500},
419     Date-Modified = {2006-03-13 17:01:15 -0500},
420     Journal = {J. Chem. Phys.},
421     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
422     Month = {September},
423     Number = {6},
424     Pages = {2102-2118},
425     Title = {Monte Carlo Study of a One-Component Plasma. I},
426     Volume = {45},
427     Year = {1966}}
428    
429     @article{Ewald21,
430     Author = {P.~P. Ewald},
431     Date-Added = {2006-03-13 13:32:04 -0500},
432 chrisfen 2636 Date-Modified = {2006-03-16 22:39:27 -0500},
433 chrisfen 2612 Journal = {Ann. Physik},
434 chrisfen 2636 Pages = {253-287},
435     Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
436 chrisfen 2612 Volume = {64},
437     Year = {1921}}
438    
439     @article{Jones56,
440     Author = {R.~E. Jones and D.~H. Templeton},
441     Date-Added = {2006-03-13 13:25:58 -0500},
442     Date-Modified = {2006-03-13 13:27:15 -0500},
443     Journal = {J. Chem. Phys.},
444     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
445     Number = {5},
446     Pages = {1062-1063},
447     Title = {Optimum Atomic Shape for Bertaut Series},
448     Volume = {25},
449     Year = {1956}}
450    
451     @article{Heyes81,
452     Author = {D.~M. Heyes},
453     Date-Added = {2006-03-13 13:12:45 -0500},
454     Date-Modified = {2006-03-13 13:14:27 -0500},
455     Journal = {J. Chem. Phys.},
456     Keywords = {Empty Keywords},
457     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
458     Number = {3},
459     Pages = {1924-1929},
460     Title = {Electrostatic potentials and fields in infinite point charge lattices},
461     Volume = {74},
462     Year = {1981}}
463    
464 chrisfen 2610 @article{Steinbach94,
465     Author = {P.~J. Steinbach and B.~R. Brooks},
466     Date-Added = {2006-03-12 19:26:45 -0500},
467     Date-Modified = {2006-03-12 19:29:43 -0500},
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