ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/multipole/multipole_2/references.bib
Revision: 4208
Committed: Fri Aug 8 15:11:49 2014 UTC (9 years, 11 months ago) by gezelter
File size: 48330 byte(s)
Log Message:
Latest

File Contents

# Content
1 %% This BibTeX bibliography file was created using BibDesk.
2 %% http://bibdesk.sourceforge.net/
3
4
5 %% Created for Dan Gezelter at 2014-08-08 10:43:40 -0400
6
7
8 %% Saved with string encoding Unicode (UTF-8)
9
10
11 @string{cpl = {Chem. Phys. Lett.}}
12
13 @string{jcp = {J. Chem. Phys.}}
14
15 @string{jctc = {J. Chem. Theory Comput.}}
16
17 @string{jpcb = {J. Phys. Chem. B}}
18
19 @string{jpcc = {J. Phys. Chem. C}}
20
21 @string{mp = {Mol. Phys.}}
22
23 @string{prl = {Phys. Rev. Lett.}}
24
25
26 @misc{supplemental,
27 Date-Added = {2014-08-08 14:43:15 +0000},
28 Date-Modified = {2014-08-08 14:43:38 +0000},
29 Title = {See Supplementary Material Document No. \underline{\hspace{1in}} for XXX.}}
30
31 @article{Izvekov:2008wo,
32 Abstract = {A short-range effective potential for long-range electrostatic interactions in homogeneously disordered condensed phase systems has been determined with a novel approach to coarse-graining in interaction space. As opposed to coarse-graining the system resolution, this approach "coarsens" the system's interactions by mapping multiple configurations of an accurate long-range atomistic potential onto a more efficient, short-range effective potential with a force-matching (FM) method. Developing an empirical potential in this manner is fundamentally different from existing strategies because it utilizes condensed-phase (as opposed to gas-phase) atomistic interactions to determine general pair potentials defined on distance meshes (as opposed to fitting predetermined functional forms). The resulting short-range (similar to 10 angstrom) effective potential reproduces structural, dynamical, and many thermodynamic properties of liquid water, ions in water, and hydrophobes in water, with unprecedented accuracy. The effective potential is also shown to be transferable to a nonaqueous molten salt system. With continued development, such effective potentials may provide an accurate and highly efficient alternative to Ewald-based long-range electrostatics methods.},
33 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
34 Author = {Izvekov, Sergei and Swanson, Jessica M. J. and Voth, Gregory A.},
35 Date = {APR 17 2008},
36 Date-Added = {2014-08-08 14:42:22 +0000},
37 Date-Modified = {2014-08-08 14:42:22 +0000},
38 Doi = {DOI 10.1021/jp710339n},
39 Journal = jpcb,
40 Pages = {4711-4724},
41 Publisher = {AMER CHEMICAL SOC},
42 Timescited = {0},
43 Title = {Coarse-graining in interaction space: A systematic approach for replacing long-range electrostatics with short-range Potentials},
44 Volume = {112},
45 Year = {2008},
46 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp710339n}}
47
48 @article{Impey82,
49 Author = {R.~W. Impey and P.~A. Madden and I.~R. McDonald},
50 Date-Added = {2014-08-08 14:29:07 +0000},
51 Date-Modified = {2014-08-08 14:29:07 +0000},
52 Journal = mp,
53 Number = {3},
54 Pages = {513-539},
55 Title = {Spectroscopic and transport properties of water: \uppercase{M}odel calculations and the interpretation of experimental results},
56 Volume = {46},
57 Year = {1982}}
58
59 @article{Perram88,
60 Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
61 Date-Added = {2014-06-06 15:36:28 +0000},
62 Date-Modified = {2014-06-06 15:36:28 +0000},
63 Journal = mp,
64 Pages = {875-893},
65 Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
66 Volume = {65},
67 Year = {1988}}
68
69 @book{openmd,
70 Author = {J. Daniel Gezelter and Madan Lamichhane and Joseph Michalka and Patrick Louden and Kelsey M. Stocker and Shenyu Kuang and James Marr and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke},
71 Date-Added = {2014-06-06 15:16:05 +0000},
72 Date-Modified = {2014-06-06 15:18:03 +0000},
73 Publisher = {An open source molecular dynamics engine},
74 Title = {OpenMD},
75 Url = {http://openmd.org (accessed 11/13/2013)},
76 Year = {version 2.2, {\tt http://openmd.org} (accessed 4/17/2014)},
77 Bdsk-Url-1 = {http://openmd.org%20(accessed%2011/13/2013)}}
78
79 @article{Nagai01081960,
80 Abstract = {The quadrupole array for the lowest energy of quadrupole interaction in crystals is obtained by generalizing Luttinger and Tisza's theory of dipole interaction. The theory is presented for the two kinds of problems: the simplest case of quadrupole pertaining to a doubly degenerate orbital eg and the other general cases both for the cubic crystals. In the former case, the quadrupole interaction is written in terms of fictitious spins, whence we can get the solution of lowest energy classically, serving to obtain some informations of the orbital ordering in compounds with Mn3+, Cu2+ and Cr2+. In the latter cases, the five components of the quadrupole are totally effective, leading to a rather complicated problem. The classical solution is, however, easily obtained, though somewhat complicated. The quadrupole array of lowest energy in face-centered cubic lattice proves to be realized in molecular crystals N2, N2O, CO2 and CO, which is accompanied with large quadrupole but without or with small dipole moment.},
81 Author = {Nagai, Ojiro and Nakamura, Tuto},
82 Date-Added = {2014-06-04 18:33:25 +0000},
83 Date-Modified = {2014-06-04 18:33:25 +0000},
84 Doi = {10.1143/PTP.24.432},
85 Journal = {Progress of Theoretical Physics},
86 Number = {2},
87 Pages = {432-454},
88 Title = {Quadrupole Interaction in Crystals},
89 Url = {http://ptp.oxfordjournals.org/content/24/2/432.abstract},
90 Volume = {24},
91 Year = {1960},
92 Bdsk-Url-1 = {http://ptp.oxfordjournals.org/content/24/2/432.abstract},
93 Bdsk-Url-2 = {http://dx.doi.org/10.1143/PTP.24.432}}
94
95 @article{Nagai01091963,
96 Author = {Nagai, Ojiro and Nakamura, Tuto},
97 Date-Added = {2014-06-04 18:33:25 +0000},
98 Date-Modified = {2014-06-04 18:33:25 +0000},
99 Doi = {10.1143/PTP.30.412a},
100 Journal = {Progress of Theoretical Physics},
101 Number = {3},
102 Pages = {412},
103 Title = {Quadrupole Interaction in Crystals},
104 Url = {http://ptp.oxfordjournals.org/content/30/3/412.1.short},
105 Volume = {30},
106 Year = {1963},
107 Bdsk-Url-1 = {http://ptp.oxfordjournals.org/content/30/3/412.1.short},
108 Bdsk-Url-2 = {http://dx.doi.org/10.1143/PTP.30.412a}}
109
110 @article{LT,
111 Author = {Luttinger, J. M. and Tisza, L.},
112 Date-Added = {2014-06-04 18:33:16 +0000},
113 Date-Modified = {2014-06-04 18:33:16 +0000},
114 Doi = {10.1103/PhysRev.70.954},
115 Issue = {11-12},
116 Journal = {Phys. Rev.},
117 Month = {Dec},
118 Pages = {954--964},
119 Publisher = {American Physical Society},
120 Title = {Theory of Dipole Interaction in Crystals},
121 Url = {http://link.aps.org/doi/10.1103/PhysRev.70.954},
122 Volume = {70},
123 Year = {1946},
124 Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.70.954},
125 Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.70.954}}
126
127 @article{LT2,
128 Author = {Luttinger, J. M. and Tisza, Laszo},
129 Date-Added = {2014-06-04 18:33:16 +0000},
130 Date-Modified = {2014-06-04 18:33:16 +0000},
131 Doi = {10.1103/PhysRev.72.257},
132 Issue = {3},
133 Journal = {Phys. Rev.},
134 Month = {Aug},
135 Pages = {257--257},
136 Publisher = {American Physical Society},
137 Title = {Errata: Theory of Dipole Interaction in Crystals [Phys. Rev. 70, 954 (1946)]},
138 Url = {http://link.aps.org/doi/10.1103/PhysRev.72.257},
139 Volume = {72},
140 Year = {1947},
141 Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.72.257},
142 Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.72.257}}
143
144 @article{Sauer,
145 Author = {Sauer, J. A.},
146 Date-Added = {2014-06-04 18:33:04 +0000},
147 Date-Modified = {2014-06-04 18:33:04 +0000},
148 Doi = {10.1103/PhysRev.57.142},
149 Issue = {2},
150 Journal = {Phys. Rev.},
151 Pages = {142--146},
152 Publisher = {American Physical Society},
153 Title = {Magnetic Energy Constants of Dipolar Lattices},
154 Url = {http://link.aps.org/doi/10.1103/PhysRev.57.142},
155 Volume = {57},
156 Year = {1940},
157 Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.57.142},
158 Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.57.142}}
159
160 @article{Chen:2004du,
161 Abstract = {Structural and thermodynamic properties of ionic fluids are related to those of a simpler "mimic" system with short ranged intermolecular interactions in a spatially varying effective field by use of local molecular field (LMF) theory, already successfully applied to nonuniform simple fluids. By consistently using the LMF approximation to describe only the slowly varying part of the Coulomb interaction, which we view as arising from a rigid Gaussian charge distribution with an appropriately chosen width a, exceptionally accurate results can be found. In this paper we study a uniform system of charged hard spheres in a uniform neutralizing background, where these ideas can be presented in their simplest form. At low densities the LMF theory reduces to a generalized version of the Poisson-Boltzmann approximation, but the predicted structure factor satisfies the exact Stillinger-Lovett moment conditions, and with optimal choice of or the lowest order approximation remains accurate for much stronger couplings. At high density and strong couplings the pair correlation function in the uniform mimic system with short ranged interactions is very similar to that of the full ionic system. A simple analytic formula can then describe the difference in internal energy between the ionic system and the associated mimic system.},
162 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
163 Author = {Chen, YG and Kaur, C and Weeks, JD},
164 Date = {DEC 23 2004},
165 Date-Added = {2014-06-04 15:12:54 +0000},
166 Date-Modified = {2014-06-04 15:12:54 +0000},
167 Doi = {DOI 10.1021/jp0469261},
168 Journal = jpcb,
169 Pages = {19874-19884},
170 Publisher = {AMER CHEMICAL SOC},
171 Timescited = {5},
172 Title = {Connecting systems with short and long ranged interactions: Local molecular field theory for ionic fluids},
173 Volume = {108},
174 Year = {2004},
175 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0469261}}
176
177 @article{Chen:2006ii,
178 Abstract = {Strong, short-ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA and lead to the formation of ion pairs in dilute ionic solutions. However, the long range of the Coulomb interactions impedes the development of a simple local picture. We address this general problem by mapping the properties of a nonuniform system with Coulomb interactions onto those of a simpler system with short-ranged intermolecular interactions in an effective external field that accounts for the averaged effects of appropriately chosen long-ranged and slowly varying components of the Coulomb interactions. The remaining short-ranged components combine with the other molecular core interactions and strongly affect pair correlations in dense or strongly coupled systems. We show that pair correlation functions in the effective short-ranged system closely resemble those in the uniform primitive model of ionic solutions and illustrate the formation of ion pairs and clusters at low densities. The theory accurately describes detailed features of the effective attraction between two equally charged walls at strong coupling and intermediate separations of the walls. Analytical results for the minimal coupling strength needed to get any attraction and for the separation at which the attractive force is a maximum are presented.},
179 Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
180 Author = {Chen, YG and Weeks, JD},
181 Date = {MAY 16 2006},
182 Date-Added = {2014-06-04 15:12:54 +0000},
183 Date-Modified = {2014-06-04 15:12:54 +0000},
184 Doi = {DOI 10.1073/pnas.0600282103},
185 Journal = pnas,
186 Keywords = {effective short-ranged model; ion pairing; mean field theory; Poission-Boltzmann},
187 Pages = {7560-7565},
188 Publisher = {NATL ACAD SCIENCES},
189 Timescited = {4},
190 Title = {Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions},
191 Volume = {103},
192 Year = {2006},
193 Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0600282103}}
194
195 @article{Denesyuk:2008ez,
196 Abstract = {We propose a simplified version of local molecular field (LMF) theory to treat Coulomb interactions in simulations of ionic fluids. LMF theory relies on splitting the Coulomb potential into a short-ranged part that combines with other short-ranged core interactions and is simulated explicitly. The averaged effects of the remaining long-ranged part are taken into account through a self-consistently determined effective external field. The theory contains an adjustable length parameter sigma that specifies the cutoff distance for the short-ranged interaction. This can be chosen to minimize the errors resulting from the mean-field treatment of the complementary long-ranged part. Here we suggest that in many cases an accurate approximation to the effective field can be obtained directly from the equilibrium charge density given by the Debye theory of screening, thus eliminating the need for a self-consistent treatment. In the limit sigma -> 0, this assumption reduces to the classical Debye approximation. We examine the numerical performance of this approximation for a simple model of a symmetric ionic mixture. Our results for thermodynamic and structural properties of uniform ionic mixtures agree well with similar results of Ewald simulations of the full ionic system. In addition, we have used the simplified theory in a grand-canonical simulation of a nonuniform ionic mixture where an ion has been fixed at the origin. Simulations using short-ranged truncations of the Coulomb interactions alone do not satisfy the exact condition of complete screening of the fixed ion, but this condition is recovered when the effective field is taken into account. We argue that this simplified approach can also be used in the simulations of more complex nonuniform systems. (c) 2008 American Institute of Physics.},
197 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
198 Author = {Denesyuk, Natalia A. and Weeks, John D.},
199 Date = {MAR 28 2008},
200 Date-Added = {2014-06-04 15:12:54 +0000},
201 Date-Modified = {2014-06-04 15:12:54 +0000},
202 Eid = {124109},
203 Journal = jcp,
204 Pages = {-},
205 Publisher = {AMER INST PHYSICS},
206 Timescited = {0},
207 Title = {A new approach for efficient simulation of {C}oulomb interactions in ionic fluids},
208 Volume = {128},
209 Year = {2008},
210 Bdsk-Url-1 = {http://dx.doi.org/124109}}
211
212 @article{Rodgers:2006nw,
213 Abstract = {Effective attraction between like-charged walls mediated by counterions is studied using local molecular field (LMF) theory. Monte Carlo simulations of the "mimic system" given by LMF theory, with short-ranged "Coulomb core" interactions in an effective single particle potential incorporating a mean-field average of the long-ranged Coulomb interactions, provide a direct test of the theory, and are in excellent agreement with more complex simulations of the full Coulomb system by Moreira and Netz [Eur. Phys. J. E 8, 33 (2002)]. A simple, generally applicable criterion to determine the consistency parameter sigma(min) needed for accurate use of the LMF theory is presented.},
214 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
215 Author = {Rodgers, Jocelyn M. and Kaur, Charanbir and Chen, Yng-Gwei and Weeks, John D.},
216 Date = {SEP 1 2006},
217 Date-Added = {2014-06-04 15:12:54 +0000},
218 Date-Modified = {2014-06-04 15:12:54 +0000},
219 Eid = {097801},
220 Journal = prl,
221 Pages = {-},
222 Publisher = {AMERICAN PHYSICAL SOC},
223 Timescited = {1},
224 Title = {Attraction between like-charged walls: Short-ranged simulations using local molecular field theory},
225 Volume = {97},
226 Year = {2006},
227 Bdsk-Url-1 = {http://dx.doi.org/097801}}
228
229 @article{Wu:044107,
230 Author = {Xiongwu Wu and Bernard R. Brooks},
231 Date-Added = {2014-06-04 15:12:16 +0000},
232 Date-Modified = {2014-06-04 15:12:16 +0000},
233 Doi = {10.1063/1.1836733},
234 Eid = {044107},
235 Journal = jcp,
236 Keywords = {Molecular Dynamics Method; Potential Energy Functions},
237 Number = {4},
238 Numpages = {18},
239 Pages = {044107},
240 Publisher = {Aip},
241 Title = {Isotropic Periodic Sum: A Method for the Calculation of Long-Range Interactions},
242 Url = {Http://Link.Aip.Org/Link/?jcp/122/044107/1},
243 Volume = {122},
244 Year = {2005},
245 Bdsk-Url-1 = {Http://Link.Aip.Org/Link/?jcp/122/044107/1},
246 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1836733}}
247
248 @article{Smith82,
249 Author = {W. Smith},
250 Date-Added = {2014-06-04 15:05:56 +0000},
251 Date-Modified = {2014-06-04 15:05:56 +0000},
252 Journal = {CCP5 Information quarterly},
253 Pages = {13-25},
254 Title = {Point multipoles in the \uppercase{E}wald summation},
255 Volume = 4,
256 Year = 1982}
257
258 @article{Smith98,
259 Author = {W. Smith},
260 Date-Added = {2014-06-04 15:05:56 +0000},
261 Date-Modified = {2014-06-04 15:05:56 +0000},
262 Journal = {CCP5 Information Quarterly},
263 Pages = {18-30},
264 Title = {Point multipoles in the \uppercase{E}wald summation (Revisited)},
265 Volume = {46},
266 Year = {1998}}
267
268 @article{Ren:2004kx,
269 Author = {Ren, Pengyu and Ponder, Jay W.},
270 Date-Added = {2014-06-04 13:47:47 +0000},
271 Date-Modified = {2014-06-04 13:47:47 +0000},
272 Doi = {10.1021/jp0484332},
273 Journal = jpcb,
274 Number = {35},
275 Pages = {13427-13437},
276 Title = {Temperature and Pressure Dependence of the AMOEBA Water Model},
277 Url = {http://pubs.acs.org/doi/abs/10.1021/jp0484332},
278 Volume = {108},
279 Year = {2004},
280 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0484332},
281 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0484332}}
282
283 @article{Ren:2003uq,
284 Author = {Ren, Pengyu and Ponder, Jay W.},
285 Date-Added = {2014-06-04 13:47:15 +0000},
286 Date-Modified = {2014-06-04 13:58:58 +0000},
287 Doi = {10.1021/jp027815+},
288 Journal = jpcb,
289 Number = {24},
290 Pages = {5933-5947},
291 Title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
292 Url = {http://pubs.acs.org/doi/abs/10.1021/jp027815\%2B},
293 Volume = {107},
294 Year = {2003},
295 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp027815%2B},
296 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp027815+}}
297
298 @article{Wang:2013fk,
299 Author = {Wang, Lee-Ping and Head-Gordon, Teresa and Ponder, Jay W. and Ren, Pengyu and Chodera, John D. and Eastman, Peter K. and Martinez, Todd J. and Pande, Vijay S.},
300 Date-Added = {2014-06-04 13:44:11 +0000},
301 Date-Modified = {2014-06-04 13:44:11 +0000},
302 Doi = {10.1021/jp403802c},
303 Journal = jpcb,
304 Number = {34},
305 Pages = {9956-9972},
306 Title = {Systematic Improvement of a Classical Molecular Model of Water},
307 Url = {http://pubs.acs.org/doi/abs/10.1021/jp403802c},
308 Volume = {117},
309 Year = {2013},
310 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp403802c},
311 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp403802c}}
312
313 @incollection{Wolf95,
314 Author = {Wolf, D.},
315 Booktitle = {Computer Simulation Studies in Condensed-Matter Physics VIII},
316 Date-Added = {2014-05-20 18:53:22 +0000},
317 Date-Modified = {2014-05-20 18:53:22 +0000},
318 Doi = {10.1007/978-3-642-79991-4_6},
319 Editor = {Landau, DavidP. and Mon, K.K. and Sch{\"u}ttler, Heinz-Bernd},
320 Isbn = {978-3-642-79993-8},
321 Language = {English},
322 Pages = {57-68},
323 Publisher = {Springer Berlin Heidelberg},
324 Series = {Springer Proceedings in Physics},
325 Title = {Simulation of Ionic Surfaces from an Absolutely Convergent Solution of the Madelung Problem},
326 Url = {http://dx.doi.org/10.1007/978-3-642-79991-4_6},
327 Volume = {80},
328 Year = {1995},
329 Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-79991-4_6}}
330
331 @article{Parry:1976fq,
332 Author = {D.E. Parry},
333 Date-Added = {2014-05-20 18:44:42 +0000},
334 Date-Modified = {2014-05-20 18:44:42 +0000},
335 Doi = {http://dx.doi.org/10.1016/0039-6028(76)90102-3},
336 Issn = {0039-6028},
337 Journal = {Surface Science},
338 Key = {tagkey1976195},
339 Number = {1},
340 Pages = {195},
341 Title = {Errata},
342 Url = {http://www.sciencedirect.com/science/article/pii/0039602876901023},
343 Volume = {54},
344 Year = {1976},
345 Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0039602876901023},
346 Bdsk-Url-2 = {http://dx.doi.org/10.1016/0039-6028(76)90102-3}}
347
348 @article{Parry:1975if,
349 Author = {D.E. Parry},
350 Date-Added = {2014-05-20 18:42:44 +0000},
351 Date-Modified = {2014-05-20 18:42:44 +0000},
352 Doi = {http://dx.doi.org/10.1016/0039-6028(75)90362-3},
353 Issn = {0039-6028},
354 Journal = {Surface Science},
355 Number = {2},
356 Pages = {433 - 440},
357 Title = {The electrostatic potential in the surface region of an ionic crystal},
358 Url = {http://www.sciencedirect.com/science/article/pii/0039602875903623},
359 Volume = {49},
360 Year = {1975},
361 Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0039602875903623},
362 Bdsk-Url-2 = {http://dx.doi.org/10.1016/0039-6028(75)90362-3}}
363
364 @article{Essmann:1995pb,
365 Author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
366 Date-Added = {2014-05-20 17:33:26 +0000},
367 Date-Modified = {2014-05-20 17:33:26 +0000},
368 Doi = {http://dx.doi.org/10.1063/1.470117},
369 Journal = jcp,
370 Number = {19},
371 Pages = {8577-8593},
372 Title = {A smooth particle mesh Ewald method},
373 Url = {http://scitation.aip.org/content/aip/journal/jcp/103/19/10.1063/1.470117},
374 Volume = {103},
375 Year = {1995},
376 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/103/19/10.1063/1.470117},
377 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.470117}}
378
379 @article{Ponder:2010vl,
380 Author = {Ponder, Jay W. and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S. and Chodera, John D. and Schnieders, Michael J. and Haque, Imran and Mobley, David L. and Lambrecht, Daniel S. and DiStasio, Robert A. and Head-Gordon, Martin and Clark, Gary N. I. and Johnson, Margaret E. and Head-Gordon, Teresa},
381 Date-Added = {2014-05-20 17:32:49 +0000},
382 Date-Modified = {2014-05-20 17:32:49 +0000},
383 Doi = {10.1021/jp910674d},
384 Journal = jpcb,
385 Note = {PMID: 20136072},
386 Number = {8},
387 Pages = {2549-2564},
388 Title = {Current Status of the AMOEBA Polarizable Force Field},
389 Url = {http://pubs.acs.org/doi/abs/10.1021/jp910674d},
390 Volume = {114},
391 Year = {2010},
392 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp910674d},
393 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp910674d}}
394
395 @article{Spohr:1997sf,
396 Author = {Spohr, E.},
397 Date-Added = {2014-05-20 17:32:27 +0000},
398 Date-Modified = {2014-05-20 17:32:27 +0000},
399 Doi = {http://dx.doi.org/10.1063/1.474295},
400 Journal = jcp,
401 Number = {16},
402 Pages = {6342-6348},
403 Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
404 Url = {http://scitation.aip.org/content/aip/journal/jcp/107/16/10.1063/1.474295},
405 Volume = {107},
406 Year = {1997},
407 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/107/16/10.1063/1.474295},
408 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.474295}}
409
410 @article{Shi:2013ij,
411 Author = {Shi, Wei and Luebke, David R.},
412 Date-Added = {2014-05-20 17:31:47 +0000},
413 Date-Modified = {2014-05-20 17:31:47 +0000},
414 Doi = {10.1021/la400226g},
415 Journal = {Langmuir},
416 Number = {18},
417 Pages = {5563-5572},
418 Title = {Enhanced Gas Absorption in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]) Confined in Silica Slit Pores: A Molecular Simulation Study},
419 Url = {http://pubs.acs.org/doi/abs/10.1021/la400226g},
420 Volume = {29},
421 Year = {2013},
422 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/la400226g},
423 Bdsk-Url-2 = {http://dx.doi.org/10.1021/la400226g}}
424
425 @article{Zahn:2002hc,
426 Author = {Zahn, Dirk and Schilling, Bernd and Kast, Stefan M.},
427 Date-Added = {2014-05-20 17:31:28 +0000},
428 Date-Modified = {2014-05-20 17:31:28 +0000},
429 Doi = {10.1021/jp025949h},
430 Journal = jpcb,
431 Number = {41},
432 Pages = {10725-10732},
433 Title = {Enhancement of the Wolf Damped Coulomb Potential:  Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
434 Url = {http://pubs.acs.org/doi/abs/10.1021/jp025949h},
435 Volume = {106},
436 Year = {2002},
437 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp025949h},
438 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp025949h}}
439
440 @article{Rhee:1989kl,
441 Author = {Rhee, Y.-J. and Halley, J. W. and Hautman, Joseph and Rahman, A.},
442 Date-Added = {2014-05-20 17:29:57 +0000},
443 Date-Modified = {2014-05-20 17:29:59 +0000},
444 Doi = {10.1103/PhysRevB.40.36},
445 Issue = {1},
446 Journal = {Phys. Rev. B},
447 Month = {Jul},
448 Numpages = {0},
449 Pages = {36--42},
450 Publisher = {American Physical Society},
451 Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
452 Url = {http://link.aps.org/doi/10.1103/PhysRevB.40.36},
453 Volume = {40},
454 Year = {1989},
455 Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevB.40.36},
456 Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevB.40.36}}
457
458 @article{Yeh:1999oq,
459 Author = {Yeh, In-Chul and Berkowitz, Max L.},
460 Date-Added = {2014-05-20 17:29:25 +0000},
461 Date-Modified = {2014-05-20 17:29:25 +0000},
462 Doi = {http://dx.doi.org/10.1063/1.479595},
463 Journal = jcp,
464 Number = {7},
465 Pages = {3155-3162},
466 Title = {Ewald summation for systems with slab geometry},
467 Url = {http://scitation.aip.org/content/aip/journal/jcp/111/7/10.1063/1.479595},
468 Volume = {111},
469 Year = {1999},
470 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/111/7/10.1063/1.479595},
471 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.479595}}
472
473 @article{Wolf:1999dn,
474 Author = {Wolf, D. and Keblinski, P. and Phillpot, S. R. and Eggebrecht, J.},
475 Date-Added = {2014-05-20 17:28:54 +0000},
476 Date-Modified = {2014-05-20 17:28:54 +0000},
477 Doi = {http://dx.doi.org/10.1063/1.478738},
478 Journal = jcp,
479 Number = {17},
480 Pages = {8254-8282},
481 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r−1 summation},
482 Url = {http://scitation.aip.org/content/aip/journal/jcp/110/17/10.1063/1.478738},
483 Volume = {110},
484 Year = {1999},
485 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/110/17/10.1063/1.478738},
486 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.478738}}
487
488 @article{Kannam:2012rr,
489 Author = {Kannam, Sridhar Kumar and Todd, B. D. and Hansen, J. S. and Daivis, Peter J.},
490 Date-Added = {2014-05-20 17:28:19 +0000},
491 Date-Modified = {2014-05-20 17:28:19 +0000},
492 Doi = {http://dx.doi.org/10.1063/1.4730167},
493 Eid = 244704,
494 Journal = jcp,
495 Number = {24},
496 Pages = {-},
497 Title = {Interfacial slip friction at a fluid-solid cylindrical boundary},
498 Url = {http://scitation.aip.org/content/aip/journal/jcp/136/24/10.1063/1.4730167},
499 Volume = {136},
500 Year = {2012},
501 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/136/24/10.1063/1.4730167},
502 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4730167}}
503
504 @article{Fennell:2006lq,
505 Author = {Fennell, Christopher J. and Gezelter, J. Daniel},
506 Date-Added = {2014-05-20 17:27:55 +0000},
507 Date-Modified = {2014-05-20 17:27:55 +0000},
508 Doi = {http://dx.doi.org/10.1063/1.2206581},
509 Eid = 234104,
510 Journal = jcp,
511 Number = {23},
512 Pages = {-},
513 Title = {Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
514 Url = {http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581},
515 Volume = {124},
516 Year = {2006},
517 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581},
518 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2206581}}
519
520 @article{Darden:1993pd,
521 Author = {Darden, Tom and York, Darrin and Pedersen, Lee},
522 Date-Added = {2014-05-20 17:27:18 +0000},
523 Date-Modified = {2014-05-20 17:27:18 +0000},
524 Doi = {http://dx.doi.org/10.1063/1.464397},
525 Journal = jcp,
526 Number = {12},
527 Pages = {10089-10092},
528 Title = {Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems},
529 Url = {http://scitation.aip.org/content/aip/journal/jcp/98/12/10.1063/1.464397},
530 Volume = {98},
531 Year = {1993},
532 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/98/12/10.1063/1.464397},
533 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.464397}}
534
535 @article{Clarke:1986eu,
536 Author = {Clarke, J. H. R. and Smith, W. and Woodcock, L. V.},
537 Date-Added = {2014-05-20 17:26:40 +0000},
538 Date-Modified = {2014-05-20 17:26:40 +0000},
539 Doi = {http://dx.doi.org/10.1063/1.450391},
540 Journal = jcp,
541 Number = {4},
542 Pages = {2290-2294},
543 Title = {Short range effective potentials for ionic fluids},
544 Url = {http://scitation.aip.org/content/aip/journal/jcp/84/4/10.1063/1.450391},
545 Volume = {84},
546 Year = {1986},
547 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/84/4/10.1063/1.450391},
548 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.450391}}
549
550 @article{Fukuda:2013sf,
551 Author = {Fukuda, Ikuo},
552 Date-Added = {2014-05-20 17:25:01 +0000},
553 Date-Modified = {2014-05-20 17:25:01 +0000},
554 Doi = {http://dx.doi.org/10.1063/1.4827055},
555 Eid = 174107,
556 Journal = jcp,
557 Number = {17},
558 Pages = {-},
559 Title = {Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system},
560 Url = {http://scitation.aip.org/content/aip/journal/jcp/139/17/10.1063/1.4827055},
561 Volume = {139},
562 Year = {2013},
563 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/139/17/10.1063/1.4827055},
564 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4827055}}
565
566 @incollection{Woodcock75,
567 Author = {Woodcock, L.V.},
568 Booktitle = {Advances in Molten Salt Chemistry},
569 Doi = {10.1007/978-1-4615-8270-0_1},
570 Editor = {Braunstein, J. and Mamantov, Gleb and Smith, G.P.},
571 Isbn = {978-1-4615-8272-4},
572 Language = {English},
573 Pages = {1-74},
574 Publisher = {Springer US},
575 Title = {Molecular Dynamics Calculations on Molten Ionic Salts},
576 Url = {http://dx.doi.org/10.1007/978-1-4615-8270-0_1},
577 Year = {1975},
578 Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-1-4615-8270-0_1}}
579
580 @article{Takada94,
581 Author = {Shimada, Jiro and Kaneko, Hiroki and Takada, Toshikazu},
582 Doi = {10.1002/jcc.540150105},
583 Issn = {1096-987X},
584 Journal = {Journal of Computational Chemistry},
585 Number = {1},
586 Pages = {28--43},
587 Publisher = {John Wiley & Sons, Inc.},
588 Title = {Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations},
589 Url = {http://dx.doi.org/10.1002/jcc.540150105},
590 Volume = {15},
591 Year = {1994},
592 Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150105}}
593
594 @article{Takada93,
595 Author = {Shimada, Jiro and Kaneko, Hiroki and Takada, Toshikazu},
596 Doi = {10.1002/jcc.540140712},
597 Issn = {1096-987X},
598 Journal = {J. Comp. Chem.},
599 Number = {7},
600 Pages = {867--878},
601 Publisher = {John Wiley & Sons, Inc.},
602 Title = {Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions},
603 Url = {http://dx.doi.org/10.1002/jcc.540140712},
604 Volume = {14},
605 Year = {1993},
606 Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540140712}}
607
608 @article{Gunsteren94,
609 Author = {Luty, Brock A. and Davis, Malcolm E. and Tironi, Ilario G. and Van Gunsteren, Wilfred F.},
610 Doi = {10.1080/08927029408022004},
611 Journal = {Mol. Simul.},
612 Number = {1},
613 Pages = {11-20},
614 Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems},
615 Url = {http://dx.doi.org/10.1080/08927029408022004},
616 Volume = {14},
617 Year = {1994},
618 Bdsk-Url-1 = {http://dx.doi.org/10.1080/08927029408022004}}
619
620 @article{Gunsteren95,
621 Author = {Luty, Brock A. and Tironi, Ilario G. and van Gunsteren, Wilfred F.},
622 Doi = {http://dx.doi.org/10.1063/1.470490},
623 Journal = jcp,
624 Number = {8},
625 Pages = {3014-3021},
626 Title = {Lattice‐sum methods for calculating electrostatic interactions in molecular simulations},
627 Url = {http://scitation.aip.org/content/aip/journal/jcp/103/8/10.1063/1.470490},
628 Volume = {103},
629 Year = {1995},
630 Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/103/8/10.1063/1.470490},
631 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.470490}}
632
633 @article{Clarke77,
634 Abstract = {Computer simulation of the (100) face of crystalline potassium chloride has been achieved using the method of molecular dynamics and a lamina model of thickness 10 ionic layers. The basic cell contained 360 ions{,} interacting via a Tosi-Fumi potential. A solution has been obtained for the long range correction to the Coulomb potential for an ionic lamina. This differs significantly from the solution for a 3-dimensional lattice.Surface distortion{,} surface energy and stress have been evaluated and agree well with experiment and previous model calculations. The ratios of surface mean square amplitudes of vibration perpendicular to the surface divided by the bulk values show an approximately 25\% anharmonic enhancement over previous calculations. The layerwise velocity autocorrelation functions yield power spectra featuring a peak for the surface mono-layer at 75 cm which compares favourably with the frequency of surface acoustic modes predicted by previous calculations.},
635 Author = {Heyes, D. M. and Barber, M. and Clarke, J. H. R.},
636 Doi = {10.1039/F29777301485},
637 Issue = {7},
638 Journal = {J. Chem. Soc.{,} Faraday Trans. 2},
639 Pages = {1485-1496},
640 Publisher = {The Royal Society of Chemistry},
641 Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
642 Url = {http://dx.doi.org/10.1039/F29777301485},
643 Volume = {73},
644 Year = {1977},
645 Bdsk-Url-1 = {http://dx.doi.org/10.1039/F29777301485}}
646
647 @article{Perram79,
648 Author = {De Leeuw, Simon W and Perram, John W},
649 Journal = mp,
650 Number = {4},
651 Pages = {1313--1322},
652 Publisher = {Taylor \& Francis},
653 Title = {Electrostatic lattice sums for semi-infinite lattices},
654 Volume = {37},
655 Year = {1979}}
656
657 @article{Smith80,
658 Abstract = {The effective interactions of ions, dipoles and higher-order multipoles under periodic boundary conditions are calculated where the array of periodic replications forms an infinite sphere surrounded by a vacuum. Discrepancies between the results of different methods of calculation are resolved and some shape-dependent effects are discussed briefly. In a simulation under these periodic boundary conditions, the net Hamiltonian contains a positive term proportional to the square of the net dipole moment of the configuration. Surrounding the infinite sphere by a continuum of dielectric constant $\epsilon'$ changes this positive term, the coefficient being zero as $\epsilon'\rightarrow\infty$. We report on the simulation of a dense fluid of hard spheres with embedded point dipoles; simulations are made for different values of $\epsilon'$, showing how the Kirkwood g-factor and the long-range part of h$_\Delta$(r) depend on $\epsilon'$ in a finite simulation. We show how this dependence on $\epsilon'$ nonetheless leads to a dielectric constant for the system that is independent of $\epsilon'$. In particular, the Clausius-Mosotti and Kirkwood formulae for the dielectric constant $\epsilon$ of the system give consistent values.},
659 Author = {{de Leeuw}, S. W. and Perram, J. W. and Smith, E. R.},
660 Doi = {10.1098/rspa.1980.0135},
661 Journal = {Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences},
662 Number = {1752},
663 Pages = {27-56},
664 Title = {Simulation of Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
665 Url = {http://rspa.royalsocietypublishing.org/content/373/1752/27.abstract},
666 Volume = {373},
667 Year = {1980},
668 Bdsk-Url-1 = {http://rspa.royalsocietypublishing.org/content/373/1752/27.abstract},
669 Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspa.1980.0135}}
670
671 @article{Wolf92,
672 Author = {Wolf, Dieter},
673 Journal = prl,
674 Number = {22},
675 Pages = {3315--3318},
676 Title = {Reconstruction of NaCl surfaces from a dipolar solution to the Madelung problem},
677 Volume = {68},
678 Year = {1992}}
679
680 @article{Acevedo13,
681 Author = {McCann, Billy W and Acevedo, Orlando},
682 Journal = jctc,
683 Number = {2},
684 Pages = {944--950},
685 Publisher = {American Chemical Society},
686 Title = {Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids},
687 Volume = {9},
688 Year = {2013}}
689
690 @article{Space12,
691 Author = {Forrest, Katherine A and Pham, Tony and McLaughlin, Keith and Belof, Jonathan L and Stern, Abraham C and Zaworotko, Michael J and Space, Brian},
692 Journal = jpcc,
693 Number = {29},
694 Pages = {15538--15549},
695 Publisher = {ACS Publications},
696 Title = {Simulation of the Mechanism of Gas Sorption in a Metal--Organic Framework with Open Metal Sites: Molecular Hydrogen in PCN-61},
697 Volume = {116},
698 Year = {2012}}
699
700 @article{English08,
701 Author = {English, Niall J},
702 Journal = mp,
703 Number = {15},
704 Pages = {1887--1898},
705 Publisher = {Taylor \& Francis},
706 Title = {Effect of electrostatics techniques on the estimation of thermal conductivity via equilibrium molecular dynamics simulation: application to methane hydrate},
707 Volume = {106},
708 Year = {2008}}
709
710 @article{Lawrence13,
711 Author = {Louden, P and Schoenborn, R and Lawrence, CP},
712 Journal = {Fluid Phase Equilibria},
713 Pages = {83--86},
714 Publisher = {Elsevier},
715 Title = {Molecular dynamics simulations of the condensation coefficient of water},
716 Volume = {349},
717 Year = {2013}}
718
719 @article{Vergne13,
720 Author = {Takashi Tokumasu and Marie-Helene Meurisse and Nicolas Fillot and Philippe Vergne},
721 Doi = {http://dx.doi.org/10.1016/j.triboint.2012.08.009},
722 Issn = {0301-679X},
723 Journal = {Tribology International},
724 Keywords = {Momentum transport},
725 Number = {0},
726 Pages = {10 - 16},
727 Title = {A molecular dynamics study of a nanoscale liquid bridge under shear},
728 Url = {http://www.sciencedirect.com/science/article/pii/S0301679X12002812},
729 Volume = {59},
730 Year = {2013},
731 Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0301679X12002812},
732 Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.triboint.2012.08.009}}
733
734 @article{Ren06,
735 Author = {Golubkov, Pavel A and Ren, Pengyu},
736 Journal = jcp,
737 Number = {6},
738 Pages = {064103},
739 Publisher = {AIP Publishing},
740 Title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
741 Volume = {125},
742 Year = {2006}}
743
744 @article{Essex10,
745 Author = {Orsi, Mario and Michel, Julien and Essex, Jonathan W},
746 Journal = {Journal of Physics: Condensed Matter},
747 Number = {15},
748 Pages = {155106},
749 Publisher = {IOP Publishing},
750 Title = {Coarse-grain modelling of DMPC and DOPC lipid bilayers},
751 Volume = {22},
752 Year = {2010}}
753
754 @article{Essex11,
755 Author = {Orsi, Mario and Essex, Jonathan W},
756 Journal = {PloS one},
757 Number = {12},
758 Pages = {e28637},
759 Publisher = {Public Library of Science},
760 Title = {The ELBA force field for coarse-grain modeling of lipid membranes},
761 Volume = {6},
762 Year = {2011}}
763
764 @article{Ichiye10_1,
765 Author = {Te, Jerez A and Tan, Ming-Liang and Ichiye, Toshiko},
766 Journal = cpl,
767 Number = {4},
768 Pages = {218--223},
769 Publisher = {Elsevier},
770 Title = {Solvation of glucose, trehalose, and sucrose by the soft-sticky dipole--quadrupole--octupole water model},
771 Volume = {491},
772 Year = {2010}}
773
774 @article{Ichiye10_2,
775 Author = {Te, Jerez A and Ichiye, Toshiko},
776 Journal = jcp,
777 Number = {11},
778 Pages = {114511},
779 Publisher = {AIP Publishing},
780 Title = {Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model},
781 Volume = {132},
782 Year = {2010}}
783
784 @article{Ichiye10_3,
785 Author = {Te, Jerez A and Ichiye, Toshiko},
786 Journal = cpl,
787 Number = {4},
788 Pages = {219--225},
789 Publisher = {Elsevier},
790 Title = {Understanding structural effects of multipole moments on aqueous solvation of ions using the soft-sticky dipole--quadrupole--octupole water model},
791 Volume = {499},
792 Year = {2010}}
793
794 @article{Gordon07,
795 Author = {Schnieders, Michael J and Baker, Nathan A and Ren, Pengyu and Ponder, Jay W},
796 Journal = jcp,
797 Number = {12},
798 Pages = {124114},
799 Publisher = {AIP Publishing},
800 Title = {Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum},
801 Volume = {126},
802 Year = {2007}}
803
804 @article{Lacman65,
805 Author = {Lacman, R.},
806 Journal = {Colloq. Int. CNRS},
807 Pages = {195},
808 Title = {Adsorption et croissance cristalline: Nancy, 6-12 Juin 1965},
809 Volume = 152,
810 Year = {1965}}
811
812 @article{PaperI,
813 Author = {Lamichhane, Madan and Gezelter, J. Daniel and Newman, Kathie E.},
814 Date-Modified = {2014-06-04 15:14:05 +0000},
815 Journal = jcp,
816 Number = {-},
817 Pages = {-},
818 Title = {Real space alternatives to the Ewald Sum. I. Taylor-shifted and Gradient-shifted electrostatics for multipoles},
819 Volume = {-},
820 Year = {2014}}
821
822 @article{fisher53,
823 Abstract = {Any topological framework requires the development of a theory of errors of characteristic and appropriate mathematical form. The paper develops a form of theory which appears to be appropriate to measurements of position on a sphere. The primary problems of estimation as applied to the true direction, and the precision of observations, are discussed in the subcases which arise. The simultaneous distribution of the amplitude and direction of the vector sum of a number of random unit vectors of given precision, is demonstrated. From this is derived the test of significance appropriate to a worker whose knowledge of precision lies entirely in the internal evidence of the sample. This is the analogue of 'Student's' test in the Gaussian theory of errors. The general formulae obtained are illustrated using measurements of the direction of remanent magnetization in the directly and inversely magnetized lava flows obtained in Iceland by Mr J. Hospers.},
824 Author = {Fisher, Ronald},
825 Doi = {10.1098/rspa.1953.0064},
826 Journal = {Proc. R. Soc. Lond. A},
827 Number = {1130},
828 Pages = {295-305},
829 Title = {Dispersion on a Sphere},
830 Url = {http://rspa.royalsocietypublishing.org/content/217/1130/295.abstract},
831 Volume = {217},
832 Year = {1953},
833 Bdsk-Url-1 = {http://rspa.royalsocietypublishing.org/content/217/1130/295.abstract},
834 Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspa.1953.0064}}
835
836 @article{Allen91,
837 Author = {Allen, F. H. and Doyle, M. J. and Taylor, R.},
838 Doi = {10.1107/S0108768190010357},
839 Journal = {Acta Crystallographica Section B},
840 Month = {Feb},
841 Number = {1},
842 Pages = {29--40},
843 Title = {{Automated conformational analysis from crystallographic data. 1. A symmetry-modified single-linkage clustering algorithm for three-dimensional pattern recognition}},
844 Url = {http://dx.doi.org/10.1107/S0108768190010357},
845 Volume = {47},
846 Year = {1991},
847 Bdsk-Url-1 = {http://dx.doi.org/10.1107/S0108768190010357}}
848
849 @article{Ewald21,
850 Author = {P.~P. Ewald},
851 Date-Added = {2006-03-13 13:32:04 -0500},
852 Date-Modified = {2006-03-16 22:39:27 -0500},
853 Journal = {Ann. Physik},
854 Pages = {253-287},
855 Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
856 Volume = {64},
857 Year = {1921}}
858
859 @article{deLeeuw80,
860 Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
861 Date-Added = {2006-03-07 10:26:31 -0500},
862 Date-Modified = {2006-03-07 10:30:11 -0500},
863 Journal = {Proc. R. Soc. London Ser. A},
864 Number = {1752},
865 Pages = {27-56},
866 Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
867 Volume = {373},
868 Year = {1980}}
869
870 @article{Smith81,
871 Author = {E.~R. Smith},
872 Date-Added = {2006-03-16 13:47:17 -0500},
873 Date-Modified = {2006-03-16 13:48:34 -0500},
874 Journal = {Proc. R. Soc. London Ser. A},
875 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
876 Pages = {475-505},
877 Title = {Electrostatic Energy in Ionic Crystals},
878 Volume = {375},
879 Year = {1981}}
880
881 @book{Allen87,
882 Address = {New York},
883 Author = {M.~P. Allen and D.~J. Tildesley},
884 Date-Modified = {2006-02-15 10:08:08 -0500},
885 Publisher = {Oxford University Press},
886 Title = {Computer Simulations of Liquids},
887 Year = 1987}
888
889 @article{Spohr97,
890 Author = {E. Spohr},
891 Date-Added = {2006-03-18 18:51:02 -0500},
892 Date-Modified = {2006-03-18 18:52:21 -0500},
893 Journal = {J. Chem. Phys.},
894 Number = {16},
895 Pages = {6342-6348},
896 Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
897 Volume = {107},
898 Year = {1997}}
899
900 @article{Yeh99,
901 Author = {I.-C. Yeh and M.~L. Berkowitz},
902 Date-Added = {2006-03-18 19:24:27 -0500},
903 Date-Modified = {2006-03-18 19:26:08 -0500},
904 Journal = {J. Chem. Phys.},
905 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
906 Number = {7},
907 Pages = {3155-3162},
908 Title = {Ewald summation for systems with slab geometry},
909 Volume = {111},
910 Year = {1999}}
911
912 @article{Kawata01,
913 Author = {M. Kawata and M. Mikami},
914 Date-Added = {2006-04-26 09:38:01 -0400},
915 Date-Modified = {2006-04-26 09:40:11 -0400},
916 Journal = {Chem. Phys. Lett.},
917 Pages = {157-164},
918 Title = {Rapid calculation of two-dimensional Ewald summation},
919 Volume = {340},
920 Year = {2001}}
921
922 @article{Arnold02,
923 Author = {A. Arnold and J. {de Joannis} and C. Holm},
924 Date-Added = {2006-04-26 09:36:09 -0400},
925 Date-Modified = {2006-04-26 09:37:52 -0400},
926 Doi = {10.1063/1.1491955},
927 Journal = {J. Chem. Phys.},
928 Number = {6},
929 Pages = {2496-2502},
930 Title = {Electrostatics in periodic slab geometries. I},
931 Volume = {117},
932 Year = {2002},
933 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1491955}}
934
935 @article{deJoannis02,
936 Author = {J. {de Joannis} and A. Arnold and C. Holm},
937 Date-Added = {2006-04-26 09:40:15 -0400},
938 Date-Modified = {2006-04-26 09:45:19 -0400},
939 Doi = {10.1063/1.1491954},
940 Journal = {J. Chem. Phys.},
941 Number = {6},
942 Pages = {2503-2512},
943 Title = {Electrostatics in periodic slab geometries. II},
944 Volume = {117},
945 Year = {2002},
946 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1491954}}
947
948 @article{Brodka04,
949 Author = {A. Br\'{o}dka},
950 Date-Added = {2006-04-26 09:41:52 -0400},
951 Date-Modified = {2006-04-26 09:43:52 -0400},
952 Doi = {10.1016/j.cplett.2004.10.086},
953 Journal = {Chem. Phys. Lett.},
954 Pages = {62-67},
955 Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
956 Volume = {400},
957 Year = {2004},
958 Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
959
960 @article{Roberts95,
961 Author = {J.~E. Roberts and J. Schnitker},
962 Date-Added = {2006-03-18 20:12:23 -0500},
963 Date-Modified = {2006-03-18 20:13:36 -0500},
964 Journal = {J. Phys. Chem.},
965 Pages = {1322-1331},
966 Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
967 Volume = {99},
968 Year = {1995}}
969
970 @article{Roberts94,
971 Author = {J.~E. Roberts and J. Schnitker},
972 Date-Added = {2006-03-18 20:10:37 -0500},
973 Date-Modified = {2006-03-18 20:12:19 -0500},
974 Journal = {J. Chem. Phys.},
975 Number = {6},
976 Pages = {5024-5031},
977 Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
978 Volume = {101},
979 Year = {1994}}
980
981 @article{Luty96,
982 Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
983 Date-Added = {2006-03-18 20:59:19 -0500},
984 Date-Modified = {2006-03-18 21:00:33 -0500},
985 Journal = {J. Phys. Chem.},
986 Number = {7},
987 Pages = {2581-2587},
988 Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
989 Volume = {100},
990 Year = {1996}}
991
992 @article{Hunenberger99a,
993 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
994 Date-Added = {2006-03-18 20:14:24 -0500},
995 Date-Modified = {2006-03-18 20:16:01 -0500},
996 Journal = {J. Chem. Phys.},
997 Number = {4},
998 Pages = {1856-1872},
999 Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
1000 Volume = {110},
1001 Year = {1999}}
1002
1003 @article{Hunenberger99b,
1004 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
1005 Date-Added = {2006-03-16 09:45:10 -0500},
1006 Date-Modified = {2006-03-18 20:16:16 -0500},
1007 Journal = {Biophys. Chem.},
1008 Pages = {69-88},
1009 Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
1010 Volume = {78},
1011 Year = {1999}}
1012
1013 @article{Weber00,
1014 Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
1015 Date-Added = {2006-03-16 09:49:22 -0500},
1016 Date-Modified = {2006-03-16 09:51:17 -0500},
1017 Doi = {10.1021/jp9937757},
1018 Journal = {J. Phys. Chem. B},
1019 Number = {15},
1020 Pages = {3668-3675},
1021 Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1022 Volume = {104},
1023 Year = {2000},
1024 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1025
1026 @article{Meineke05,
1027 Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
1028 Date-Modified = {2006-03-05 12:37:31 -0500},
1029 Journal = {J. Comp. Chem.},
1030 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
1031 Pages = {252-271},
1032 Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
1033 Volume = 26,
1034 Year = 2005}