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Comparing trunk/electrostaticMethodsPaper/electrostaticMethods.bib (file contents):
Revision 2575 by chrisfen, Sat Jan 28 22:42:46 2006 UTC vs.
Revision 2612 by chrisfen, Mon Mar 13 22:59:52 2006 UTC

#	Line 1 | Line 1
1	<	@string{jcp = "J. Chem. Phys."}
2	<	@string{cpl = "Chem. Phys. Lett."}
3	<	@string{jpc = "J. Phys. Chem."}
4	<	@string{jpcA = "J. Phys. Chem. A"}
5	<	@string{jpcB = "J. Phys. Chem. B"}
6	<	@string{cp  = "Chem. Phys."}
7	<	@string{acp = "Adv. Chem. Phys."}
8	<	@string{pra = "Phys. Rev. A"}
9	<	@string{prb = "Phys. Rev. B"}
10	<	@string{pre = "Phys. Rev. E"}
11	<	@string{prl = "Phys. Rev. Lett."}
12	<	@string{rmp = "Rev. Mod. Phys."}
13	<	@string{jml = "J. Mol. Liq."}
14	<	@string{mp = "Mol. Phys."}
15	<	@string{pnas = "Proc. Natl. Acad. Sci. USA"}
16	<	@string{jacs = "J. Am. Chem. Soc."}
17	<	@string{jcc = "J. Comput. Chem."}
18	<	@string{pccp = "Phys. Chem. Chem. Phys."}
1	>	%% This BibTeX bibliography file was created using BibDesk.
2	>	%% http://bibdesk.sourceforge.net/
3
20	–	@Book{Berne90,
21	–	author =       {B.~J. Berne and R. Pecora},
22	–	title =        {Dynamic Light Scattering},
23	–	publisher =    {Robert E. Krieger Publishing Company, Inc.},
24	–	year =         1990,
25	–	address =      {Malabar, Florida}
26	–	}
4
5	<	@Article{Evans77,
29	<	author =       {D.~J. Evans},
30	<	title =        {On the representation of orientation space},
31	<	journal =      {Mol. Phys.},
32	<	year =         1977,
33	<	volume =       34,
34	<	pages =        {317-325}
35	<	}
5	>	%% Created for Chris Fennell at 2006-03-13 17:01:21 -0500
6
37	–	@Article{Tuckerman92,
38	–	author =       {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
39	–	title =        {Reversible multiple time scale molecular dynamics},
40	–	journal =      jcp,
41	–	year =         1992,
42	–	volume =       97,
43	–	pages =        {1990-2001}
44	–	}
7
8	<	@Book{Hansen86,
47	<	author =       {J.~P. Hansen and I.~R. McDonald},
48	<	title =        {Theory of Simple Liquids},
49	<	chapter =      7,
50	<	publisher =    {Academic Press},
51	<	year =         1986,
52	<	address =      {London},
53	<	pages =        {199-206}
54	<	}
8	>	%% Saved with string encoding Western (ASCII)
9
56	–	@Article{Angelani98,
57	–	author =       {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
58	–	title =        {Connected Network of Minima as a Model Glass: Long
59	–	Time Dynamics},
60	–	journal =      prl,
61	–	year =         1998,
62	–	volume =       81,
63	–	number =       21,
64	–	pages =        {4648-4651}
65	–	}
10
11	<	@Article{Stillinger82,
68	<	author =       {F.~H. Stillinger and T.~A. Weber},
69	<	title =        {Hidden structure in liquids},
70	<	journal =      pra,
71	<	year =         1982,
72	<	volume =       25,
73	<	number =       2,
74	<	pages =        {978-989}
75	<	}
11	>	@STRING{acp = "Adv. Chem. Phys."}
12
13	<	@Article{Stillinger83,
78	<	author =       {F.~H. Stillinger and T.~A. Weber},
79	<	title =        {Dynamics of structural transitions in liquids},
80	<	journal =      pra,
81	<	year =         1983,
82	<	volume =       28,
83	<	number =       4,
84	<	pages =        {2408-2416}
85	<	}
13	>	@STRING{cp = "Chem. Phys."}
14
15	<	@Article{Weber84,
88	<	author =       {T.~A. Weber and F.~H. Stillinger},
89	<	title =        {The effect of density on the inherent structure in
90	<	liquids},
91	<	journal =      jcp,
92	<	year =         1984,
93	<	volume =       80,
94	<	number =       6,
95	<	pages =        {2742-2746}
96	<	}
15	>	@STRING{cpl = "Chem. Phys. Lett."}
16
17	<	@Article{Stillinger85,
99	<	author =       {F.~H. Stillinger and T.~A. Weber},
100	<	title =        {Inherent structure theory of liquids in the
101	<	hard-sphere limit},
102	<	journal =      jcp,
103	<	year =         1985,
104	<	volume =       83,
105	<	number =       9,
106	<	pages =        {4767-4775}
107	<	}
17	>	@STRING{jacs = "J. Am. Chem. Soc."}
18
19	<	@Article{Stillinger98,
110	<	author =       {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
111	<	title =        {Signatures of distinct dynamical regimes in the
112	<	energy landscape of a glass-forming liquid},
113	<	journal =      {Nature},
114	<	year =         1998,
115	<	volume =       393,
116	<	pages =        {554-557}
117	<	}
19	>	@STRING{jcc = "J. Comput. Chem."}
20
21	+	@STRING{jcp = "J. Chem. Phys."}
22
23	<	@Article{Parkhurst75a,
121	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
122	<	title =        {Dense liquids. I. The effect of density and
123	<	temperature on viscosity of tetramethylsilane and
124	<	benzene-$\mbox{D}_6$},
125	<	journal =      jcp,
126	<	year =         1975,
127	<	volume =       63,
128	<	number =       6,
129	<	pages =        {2698-2704}
130	<	}
23	>	@STRING{jml = "J. Mol. Liq."}
24
25	<	@Article{Parkhurst75b,
133	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
134	<	title =        {Dense liquids. II. The effect of density and
135	<	temperature on viscosity of tetramethylsilane and
136	<	benzene },
137	<	journal =      jcp,
138	<	year =         1975,
139	<	volume =       63,
140	<	number =       6,
141	<	pages =        {2705-2709}
142	<	}
25	>	@STRING{jpc = "J. Phys. Chem."}
26
27	<	@Article{Forester97,
145	<	author =       {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
146	<	title =        {Antibiotic activity of valinomycin - Molecular
147	<	dynamics simulations involving the water/membrane
148	<	interface},
149	<	journal =      {J. Chem. Soc. - Faraday Transactions},
150	<	year =         1997,
151	<	volume =       93,
152	<	pages =        {613-619}
153	<	}
27	>	@STRING{jpca = "J. Phys. Chem. A"}
28
29	<	@Article{Tieleman98,
156	<	author =       {D.~P. Tieleman and H.~J.~C. Berendsen},
157	<	title =        {A molecular dynamics study of the pores formed by
158	<	Escherichia coli OmpF porin in a fully hydrated
159	<	palmitoyloleoylphosphatidylcholine bilayer},
160	<	journal =      {Biophys. J.},
161	<	year =         1998,
162	<	volume =       74,
163	<	pages =        {2786-2801}
164	<	}
29	>	@STRING{jpcb = "J. Phys. Chem. B"}
30
31	<	@Article{Cascales98,
167	<	author =       {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
168	<	title =        {Anaesthetic mechanism on a model biological
169	<	membrane: A molecular dynamics simulation study},
170	<	journal =      {J. Phys. Chem. B},
171	<	year =         1998,
172	<	volume =       102,
173	<	pages =        {625-631}
174	<	}
31	>	@STRING{mp = "Mol. Phys."}
32
33	<	@Article{Bassolino95,
177	<	author =       {D. Bassolino and H.~E. Alper and T.~R. Stouch},
178	<	title =        {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID
179	<	BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
180	<	journal =      {J. Am. Chem. Soc.},
181	<	year =         1995,
182	<	volume =       117,
183	<	pages =        {4118-4129}
184	<	}
33	>	@STRING{pccp = "Phys. Chem. Chem. Phys."}
34
35	<	@Article{Alper95,
187	<	author =       {H.~E. Alper and T.~R. Stouch},
188	<	title =        {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN
189	<	BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
190	<	journal =      {J. Phys. Chem.},
191	<	year =         1995,
192	<	volume =       99,
193	<	pages =        {5724-5731}
194	<	}
35	>	@STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36
37	<	@Article{Sok92,
197	<	author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
198	<	title =        {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
199	<	SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
200	<	journal =      {J. Chem. Phys.},
201	<	year =         1992,
202	<	volume =       96,
203	<	pages =        {4699-4704}
204	<	}
37	>	@STRING{pra = "Phys. Rev. A"}
38
39	<	@Article{Rabani99,
207	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
208	<	title =        {Direct Observation of Stretched-Exponential
209	<	Relaxation in Low-Temperature Lennard-Jones Systems
210	<	Using the Cage Correlation Function},
211	<	journal =      prl,
212	<	year =         {1999},
213	<	volume =       82,
214	<	pages =        {3649}
215	<	}
39	>	@STRING{prb = "Phys. Rev. B"}
40
41	<	@Article{Rabani97,
218	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
219	<	title =        {Calculating the hopping rate for self-diffusion on
220	<	rough potential energy surfaces: Cage correlations},
221	<	journal =      {J. Chem. Phys.},
222	<	year =         1997,
223	<	volume =       107,
224	<	pages =        {6867-6876}
225	<	}
41	>	@STRING{pre = "Phys. Rev. E"}
42
43	<	@Article{Gezelter99,
228	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
229	<	title =        {Methods for calculating the hopping rate for
230	<	orientational and spatial diffusion in a molecular
231	<	liquid: $\mbox{CS}_{2}$},
232	<	journal =      jcp,
233	<	year =         1999,
234	<	volume =       110,
235	<	pages =        3444
236	<	}
43	>	@STRING{prl = "Phys. Rev. Lett."}
44
45	<	@Article{Gezelter98a,
239	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
240	<	title =        {Response to 'Comment on a Critique of the
241	<	Instantaneous Normal Mode (INM) Approach to
242	<	Diffusion'},
243	<	journal =      jcp,
244	<	year =         1998,
245	<	volume =       109,
246	<	pages =        4695
247	<	}
45	>	@STRING{rmp = "Rev. Mod. Phys."}
46
249	–	@Article{Gezelter97,
250	–	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
251	–	title =        {Can imaginary instantaneous normal mode frequencies
252	–	predict barriers to self-diffusion?},
253	–	journal =      jcp,
254	–	year =         1997,
255	–	volume =       107,
256	–	pages =        4618
257	–	}
47
48	<	@Article{Zwanzig83,
49	<	author =       {R. Zwanzig},
50	<	title =        {On the relation between self-diffusion and viscosity
51	<	of liquids},
52	<	journal =      jcp,
53	<	year =         1983,
54	<	volume =       79,
55	<	pages =        {4507-4508}
56	<	}
57	<
58	<	@Article{Zwanzig88,
59	<	author =       {R. Zwanzig},
271	<	title =        {Diffusion in rough potential},
272	<	journal =      {Proc. Natl. Acad. Sci. USA},
273	<	year =         1988,
274	<	volume =       85,
275	<	pages =        2029
276	<	}
48	>	@article{Brush66,
49	>	Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
50	>	Date-Added = {2006-03-13 16:55:39 -0500},
51	>	Date-Modified = {2006-03-13 17:01:15 -0500},
52	>	Journal = {J. Chem. Phys.},
53	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
54	>	Month = {September},
55	>	Number = {6},
56	>	Pages = {2102-2118},
57	>	Title = {Monte Carlo Study of a One-Component Plasma. I},
58	>	Volume = {45},
59	>	Year = {1966}}
60
61	<	@Article{Stillinger95,
62	<	author =       {F.~H. Stillinger},
63	<	title =        {A Topographic View of Supercooled Liquids and Glass
64	<	Formation},
65	<	journal =      {Science},
66	<	year =         1995,
67	<	volume =       267,
68	<	pages =        {1935-1939}
286	<	}
61	>	@article{Ewald21,
62	>	Author = {P.~P. Ewald},
63	>	Date-Added = {2006-03-13 13:32:04 -0500},
64	>	Date-Modified = {2006-03-13 13:32:55 -0500},
65	>	Journal = {Ann. Physik},
66	>	Pages = {253},
67	>	Volume = {64},
68	>	Year = {1921}}
69
70	<	@InCollection{Angell85,
71	<	author =       {C.~A. Angell},
72	<	title =        {unknown},
73	<	booktitle =    {Relaxations in Complex Systems},
74	<	publisher =    {National Technical Information Service,
75	<	U.S. Department of Commerce},
76	<	year =         1985,
77	<	editor =       {K.~Ngai and G.~B. Wright},
78	<	address =      {Springfield, VA},
79	<	pages =        1
80	<	}
70	>	@article{Jones56,
71	>	Author = {R.~E. Jones and D.~H. Templeton},
72	>	Date-Added = {2006-03-13 13:25:58 -0500},
73	>	Date-Modified = {2006-03-13 13:27:15 -0500},
74	>	Journal = {J. Chem. Phys.},
75	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
76	>	Number = {5},
77	>	Pages = {1062-1063},
78	>	Title = {Optimum Atomic Shape for Bertaut Series},
79	>	Volume = {25},
80	>	Year = {1956}}
81
82	<	@Article{Bembenek96,
83	<	author =       {S.~D. Bembenek and B.~B. Laird},
84	<	title =        {The role of localization in glasses and supercooled liquids},
85	<	journal =      jcp,
86	<	year =         1996,
87	<	volume =       104,
88	<	pages =        5199
89	<	}
82	>	@article{Heyes81,
83	>	Author = {D.~M. Heyes},
84	>	Date-Added = {2006-03-13 13:12:45 -0500},
85	>	Date-Modified = {2006-03-13 13:14:27 -0500},
86	>	Journal = {J. Chem. Phys.},
87	>	Keywords = {Empty Keywords},
88	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
89	>	Number = {3},
90	>	Pages = {1924-1929},
91	>	Title = {Electrostatic potentials and fields in infinite point charge lattices},
92	>	Volume = {74},
93	>	Year = {1981}}
94
95	<	@Article{Sun97,
96	<	author =       {X. Sun and W.~H. Miller},
97	<	title =        {Semiclassical initial value representation for
98	<	electronically nonadiabatic molecular dynamics},
99	<	journal =      jcp,
100	<	year =         1997,
101	<	volume =       106,
102	<	pages =        6346
103	<	}
95	>	@article{Steinbach94,
96	>	Author = {P.~J. Steinbach and B.~R. Brooks},
97	>	Date-Added = {2006-03-12 19:26:45 -0500},
98	>	Date-Modified = {2006-03-12 19:29:43 -0500},
99	>	Doi = {10.1002/jcc.540150702},
100	>	Journal = {J. Comput. Chem.},
101	>	Number = {7},
102	>	Pages = {667-683},
103	>	Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
104	>	Volume = {15},
105	>	Year = {1994}}
106
107	<	@Article{Spath96,
108	<	author =       {B.~W. Spath and W.~H. Miller},
109	<	title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
110	<	PROBABILITIES},
111	<	journal =      jcp,
112	<	year =         1996,
113	<	volume =       104,
114	<	pages =        95
115	<	}
107	>	@article{deLeeuw80,
108	>	Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
109	>	Date-Added = {2006-03-07 10:26:31 -0500},
110	>	Date-Modified = {2006-03-07 10:30:11 -0500},
111	>	Journal = {Proc. R. Soc. London Ser. A},
112	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
113	>	Number = {1752},
114	>	Pages = {27-56},
115	>	Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
116	>	Volume = {373},
117	>	Year = {1980}}
118
119	<	@Book{Warshel91,
120	<	author =       {Arieh Warshel},
121	<	title =        {Computer modeling of chemical reactions in enzymes
122	<	and solutions},
123	<	publisher =    {Wiley},
124	<	year =         1991,
125	<	address =      {New York}
126	<	}
119	>	@article{Essmann95,
120	>	Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
121	>	Date-Added = {2006-03-05 12:25:25 -0500},
122	>	Date-Modified = {2006-03-05 12:29:07 -0500},
123	>	Journal = {J. Chem. Phys.},
124	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
125	>	Number = {19},
126	>	Pages = {8577-8593},
127	>	Title = {A smooth particle mesh Ewald method},
128	>	Volume = {103},
129	>	Year = {1995}}
130
131	<	@Article{Vuilleumier97,
132	<	author =       {Rodolphe Vuilleumier and Daniel Borgis},
133	<	title =        {Molecular Dynamics of an excess proton in water
134	<	using a non-additive valence bond force field},
135	<	journal =      jpc,
136	<	year =         1997,
137	<	volume =       {in press}
138	<	}
131	>	@article{Kast03,
132	>	Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
133	>	Date-Added = {2006-02-18 16:47:26 -0500},
134	>	Date-Modified = {2006-02-18 16:51:25 -0500},
135	>	Journal = {Chem. Phys. Lett.},
136	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
137	>	Pages = {398-404},
138	>	Title = {Integral equation theory for correcting truncation errors in molecular simulations},
139	>	Volume = {367},
140	>	Year = {2003}}
141
142	<	@Article{Kob95a,
143	<	author =       {W. Kob and H.~C. Andersen},
144	<	title =        {Testing mode-coupling theory for a supercooled
145	<	binary Lennard-Jones mixtures: The van Hove
146	<	corraltion function},
147	<	journal =      pre,
148	<	year =         1995,
149	<	volume =       51,
150	<	pages =        {4626-4641}
151	<	}
142	>	@article{Tobias01,
143	>	Author = {D.~J. Tobias},
144	>	Date-Added = {2006-02-15 11:28:58 -0500},
145	>	Date-Modified = {2006-02-15 11:32:16 -0500},
146	>	Journal = {Curr. Opin. Struct. Biol.},
147	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
148	>	Pages = {253-261},
149	>	Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
150	>	Volume = {11},
151	>	Year = {2001}}
152
153	<	@Article{Kob95b,
154	<	author =       {W. Kob and H.~C. Andersen},
155	<	title =        {Testing mode-coupling theory for a supercooled
156	<	binary Lennard-Jones mixtures. II. Intermediate
157	<	scattering function and dynamic susceptibility},
158	<	journal =      pre,
159	<	year =         1995,
160	<	volume =       52,
161	<	pages =        {4134-4153}
162	<	}
153	>	@article{Zahn02,
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1705	<	journal =      {Journal of Computational Physics},
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1708	<	pages =        {327-341}
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1709	>	Year = 1991}
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1712	+	Author = {S.~J Marrink and H.~J.~C. Berendsen},
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1722	<	title =        {Analytical Mechanics},
1723	<	chapter =      10,
1724	<	publisher =    {Saunders College Publishing},
1725	<	address =      {},
1726	<	year =         1999,
2002	<	edition =      {6th}
2003	<	}
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1721	>	Author = {Murray~S. Daw},
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1724	>	Title = {Model of metallic cohesion: The embedded-atom method},
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1726	>	Year = 1989}
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1730	<	title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1731	<	journal =      {Biophysical Journal},
1732	<	year =         2000,
1733	<	volume =       79,
1734	<	pages =        {3172-3192}
1735	<	}
1728	>	@inbook{Voter95b,
1729	>	Author = {A.~F. Voter},
1730	>	Chapter = 4,
1731	>	Date-Modified = {2006-02-15 10:35:07 -0500},
1732	>	Editor = {J.~H. Westbrook and R.~L. Fleischer},
1733	>	Pages = 77,
1734	>	Publisher = {John Wiley and Sons Ltd},
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1737	>	Year = 1995}
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1740	<	author =       {E. Egberts and H.~J.~C. Berendsen},
1741	<	title =        {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1742	<	journal =      {J. Chem. Phys.},
1743	<	year =         1988,
1744	<	volume =       89,
1745	<	pages =        {3718-3732}
1746	<	}
1739	>	@article{Marrink02,
1740	>	Author = {S.~J. Marrink and D.~P. Teileman},
1741	>	Date-Modified = {2006-02-15 10:28:20 -0500},
1742	>	Journal = {Biophysical Journal},
1743	>	Pages = {2386-2392},
1744	>	Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1745	>	Volume = 83,
1746	>	Year = 2002}
1747
1748	<	@Article{Holz00,
1749	<	author =       {M. Holz and S.~R. Heil and A. Sacco},
1750	<	title =        {Temperature-dependent self-diffusion coefficients of
1751	<	water and six selected molecular liquids for calibration
1752	<	in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1753	<	journal =      {Phys. Chem. Chem. Phys.},
1754	<	year =         2000,
1755	<	volume =       2,
2031	<	pages =        {4740-4742},
2032	<	}
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1750	>	Date-Modified = {2006-02-15 10:11:01 -0500},
1751	>	Journal = {Biophysical Journal},
1752	>	Pages = {3636-3645},
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1758	<	author =       {C. Zannoni},
1759	<	title =        {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1760	<	booktitle =    {The Molecular Dynamics of Liquid Crstals},
1761	<	pages =        {139-169},
1762	<	publisher =    {Kluwer Academic Publishers},
1763	<	year =         1994,
1764	<	editor =       {G.~R. Luckhurst and C.~A. Veracini},
2042	<	chapter =      6
2043	<	}
1757	>	@article{Gomez03,
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1761	>	Pages = {217-227},
1762	>	Title = {Setting up and optimization of membrane protein simulations},
1763	>	Volume = 31,
1764	>	Year = 2002}
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1766	+	@article{Smondyrev99,
1767	+	Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1768	+	Date-Modified = {2006-02-15 10:10:29 -0500},
1769	+	Journal = {Biophysical Journal},
1770	+	Pages = {2472-2478},
1771	+	Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1772	+	Volume = 76,
1773	+	Year = 1999}
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1775	<	@Article{melchionna93,
1776	<	author =       {S. Melchionna and G. Ciccotti and B.~L. Holian},
1777	<	title =        {Hoover {\sc npt} dynamics for systems varying in shape and size},
1778	<	journal =      {Molecular Physics},
1779	<	year =         1993,
1780	<	volume =       78,
1781	<	pages =        {533-544}
1782	<	}
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1778	>	Journal = {J. Phys. Chem. B},
1779	>	Pages = {3696-3705},
1780	>	Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1781	>	Volume = 106,
1782	>	Year = 2002}
1783
1784	+	@article{Norberg00,
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1787	+	Journal = {Biophysical Journal},
1788	+	Pages = {1537-1553},
1789	+	Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1790	+	Volume = 79,
1791	+	Year = 2000}
1792
1793	+	@article{Patra03,
1794	+	Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1795	+	Date-Modified = {2006-02-15 10:29:58 -0500},
1796	+	Journal = {Biophysical Journal},
1797	+	Pages = {3636-3645},
1798	+	Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1799	+	Volume = 84,
1800	+	Year = 2003}
1801
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1803	<	author =       {C.~J. Fennell and J.~D. Gezelter},
1804	<	title =        {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1805	<	journal =      jcp,
1806	<	year =         2004,
1807	<	volume =       120,
1808	<	number =       19,
1809	<	pages =        {9175-9184}
2065	<	}
1802	>	@article{Marrink04,
1803	>	Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1804	>	Date-Modified = {2006-02-15 10:28:28 -0500},
1805	>	Journal = {J. Phys. Chem. B},
1806	>	Pages = {750-760},
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1809	>	Year = 2004}
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1813	<	title =        {A coarse Grain Model for Phospholipid Simulations},
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1815	<	year =         2001,
1816	<	volume =       105,
1817	<	pages =        {4464-4470}
1818	<	}
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1813	>	Date-Modified = {2006-02-15 10:08:20 -0500},
1814	>	Journal = {Journal of Computational Physics},
1815	>	Pages = {24-34},
1816	>	Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1817	>	Volume = 52,
1818	>	Year = 1983}
1819
1820	+	@article{Hura00,
1821	+	Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
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1823	+	Journal = {J. Chem. Phys.},
1824	+	Pages = {9140-9148},
1825	+	Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1826	+	Volume = 113,
1827	+	Year = 2000}
1828
1829	<	@Article{marrink03:vesicles,
1830	<	author =       {S.~J. Marrink and A.~E. Mark},
1831	<	title =        {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1832	<	journal =      {J. Am. Chem. Soc.},
1833	<	year =         2003,
1834	<	volume =       125,
1835	<	pages =        {15233-15242}
1836	<	}
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1830	>	Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1831	>	Date-Modified = {2006-02-15 10:31:44 -0500},
1832	>	Journal = {Journal of Computational Physics},
1833	>	Pages = {327-341},
1834	>	Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1835	>	Volume = 23,
1836	>	Year = 1977}
1837
1838	<	@Article{FletcherReeves,
1839	<	author =       {R. Fletcher and C.~M. Reeves},
1840	<	title =        {Function minimization by conjugate gradients},
1841	<	journal =      {Comput. J.},
1842	<	year =         1964,
1843	<	volume =       7,
1844	<	number =       2,
1845	<	pages =        {149-154}
2094	<	}
1838	>	@inbook{Fowles99,
1839	>	Author = {G.~R. Fowles and G.~L. Cassiday},
1840	>	Chapter = 10,
1841	>	Date-Modified = {2006-02-15 10:18:00 -0500},
1842	>	Edition = {6th},
1843	>	Publisher = {Saunders College Publishing},
1844	>	Title = {Analytical Mechanics},
1845	>	Year = 1999}
1846
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1849	<	title =        {Note sur la convergence de methodes de directions conjugees},
1850	<	journal =      {Rev. Fr. Inform. Rech. Oper.},
1851	<	year =         1969,
1852	<	volume =       {16-R1},
1853	<	pages =        {35-43}
1854	<	}
1847	>	@article{Petrache00,
1848	>	Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1849	>	Date-Modified = {2006-02-15 10:30:24 -0500},
1850	>	Journal = {Biophysical Journal},
1851	>	Pages = {3172-3192},
1852	>	Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1853	>	Volume = 79,
1854	>	Year = 2000}
1855
1856	<	@article{Voter:87,
1857	<	Author = {A.F. Voter and S.P. Chen},
1856	>	@article{Egberts88,
1857	>	Author = {E. Egberts and H.~J.~C. Berendsen},
1858	>	Date-Modified = {2006-02-15 10:16:43 -0500},
1859	>	Journal = {J. Chem. Phys.},
1860	>	Pages = {3718-3732},
1861	>	Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1862	>	Volume = 89,
1863	>	Year = 1988}
1864	>
1865	>	@article{Holz00,
1866	>	Author = {M. Holz and S.~R. Heil and A. Sacco},
1867	>	Journal = {Phys. Chem. Chem. Phys.},
1868	>	Pages = {4740-4742},
1869	>	Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1870	>	Volume = 2,
1871	>	Year = 2000}
1872	>
1873	>	@incollection{Zannoni94,
1874	>	Author = {C. Zannoni},
1875	>	Booktitle = {The Molecular Dynamics of Liquid Crstals},
1876	>	Chapter = 6,
1877	>	Date-Modified = {2006-02-15 10:12:36 -0500},
1878	>	Editor = {G.~R. Luckhurst and C.~A. Veracini},
1879	>	Pages = {139-169},
1880	>	Publisher = {Kluwer Academic Publishers},
1881	>	Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1882	>	Year = 1994}
1883	>
1884	>	@article{Melchionna93,
1885	>	Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
1886	>	Date-Modified = {2006-02-15 10:28:54 -0500},
1887	>	Journal = {Molecular Physics},
1888	>	Pages = {533-544},
1889	>	Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
1890	>	Volume = 78,
1891	>	Year = 1993}
1892	>
1893	>	@article{Fennell04,
1894	>	Author = {C.~J. Fennell and J.~D. Gezelter},
1895	>	Date-Modified = {2006-02-15 09:08:04 -0500},
1896	>	Journal = jcp,
1897	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
1898	>	Number = 19,
1899	>	Pages = {9175-9184},
1900	>	Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1901	>	Volume = 120,
1902	>	Year = 2004}
1903	>
1904	>	@article{Klein01,
1905	>	Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
1906	>	Date-Modified = {2006-02-15 10:27:22 -0500},
1907	>	Journal = {J. Phys. Chem. B},
1908	>	Pages = {4464-4470},
1909	>	Title = {A Coarse Grain Model for Phospholipid Simulations},
1910	>	Volume = 105,
1911	>	Year = 2001}
1912	>
1913	>	@article{Marrink03,
1914	>	Author = {S.~J. Marrink and A.~E. Mark},
1915	>	Date-Modified = {2006-02-15 10:28:41 -0500},
1916	>	Journal = {J. Am. Chem. Soc.},
1917	>	Pages = {15233-15242},
1918	>	Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1919	>	Volume = 125,
1920	>	Year = 2003}
1921	>
1922	>	@article{Fletcher64,
1923	>	Author = {R. Fletcher and C.~M. Reeves},
1924	>	Date-Modified = {2006-02-15 10:17:34 -0500},
1925	>	Journal = {Comput. J.},
1926	>	Number = 2,
1927	>	Pages = {149-154},
1928	>	Title = {Function minimization by conjugate gradients},
1929	>	Volume = 7,
1930	>	Year = 1964}
1931	>
1932	>	@article{Polak69,
1933	>	Author = {E. Polak and G. Ribiere},
1934	>	Date-Modified = {2006-02-15 10:14:00 -0500},
1935	>	Journal = {Rev. Fr. Inform. Rech. Oper.},
1936	>	Pages = {35-43},
1937	>	Title = {Note sur la convergence de methodes de directions conjugees},
1938	>	Volume = {16-R1},
1939	>	Year = 1969}
1940	>
1941	>	@article{Voter87,
1942	>	Author = {A.~F. Voter and S.~P. Chen},
1943	>	Date-Modified = {2006-02-15 10:35:19 -0500},
1944		Journal = {Mat. Res. Soc. Symp. Proc.},
1945		Pages = {175},
1946		Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
1947		Volume = {82},
1948		Year = {1987}}
1949
1950	<	@article{Hendrickson:95,
1950	>	@article{Hendrickson95,
1951		Author = {Bruce Hendrickson and Steve Plimpton},
1952	+	Date-Modified = {2006-02-15 10:19:11 -0500},
1953		Journal = {Journal of Parallel and Distributed Computing},
1954		Pages = {15-25},
1955		Title = {Parallel Many-body Simulations without All-to-All Communication},
1956		Volume = {27},
1957		Year = {1995}}
1958
1959	+	@inproceedings{Paradyn93,
1960	+	Address = {Pittsburgh, PA},
1961	+	Author = {S.~J. Plimpton and B.~A. Hendrickson},
1962	+	Booktitle = {Materials Theory and Modelling},
1963	+	Date-Modified = {2006-02-15 10:30:42 -0500},
1964	+	Editor = {J. Broughton and P. Bristowe and J. Newsam},
1965	+	Pages = 37,
1966	+	Publisher = {Materials Research Society},
1967	+	Series = {MRS Proceedings},
1968	+	Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
1969	+	Volume = 291,
1970	+	Year = 1993}
1971
1972	<
1973	<	@InProceedings{Paradyn,
1974	<	author =       {S.~J. Plimpton and B.~A. Hendrickson},
2125	<	title =        {Parallel Molecular Dynamics With the Embedded Atom Method},
2126	<	booktitle =    {Materials Theory and Modelling},
2127	<	pages =        37,
2128	<	year =         1993,
2129	<	editor =       {J. Broughton and P. Bristowe and J. Newsam},
2130	<	volume =       291,
2131	<	series =       {MRS Proceedings},
2132	<	address =      {Pittsburgh, PA},
2133	<	publisher =    {Materials Research Society}
2134	<	}
2135	<
2136	<	@article{Voter:95,
2137	<	Author = {A.F. Voter},
1972	>	@article{Voter95a,
1973	>	Author = {A.~F. Voter},
1974	>	Date-Modified = {2006-02-15 10:35:27 -0500},
1975		Journal = {Intermetallic Compounds: Principles and Practice},
1976		Pages = {77},
1977		Title = {The Embedded-Atom Method},
1978		Volume = {1},
1979		Year = {1995}}
1980
1981	<	@article{Heller:90,
1981	>	@article{Heller90,
1982		Author = {H. Heller and H. Grubmuller and K. Schulten},
1983	+	Date-Modified = {2006-02-15 10:19:02 -0500},
1984		Journal = {Molecular Simulation},
1985		Pages = {133},
1986		Title = {Molecular dynamics simulation on a parallel computer},
1987		Volume = {5},
1988		Year = {1990}}
1989
1990	<	@Book{Fox88,
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1992	<	title =        {Solving Promblems on Concurrent Processors},
1993	<	publisher =    {Prentice-Hall},
1994	<	year =         1988,
1995	<	volume =       {I},
1996	<	address =      {Englewood Cliffs, NJ}
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1990	>	@book{Fox88,
1991	>	Address = {Englewood Cliffs, NJ},
1992	>	Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
1993	>	Publisher = {Prentice-Hall},
1994	>	Title = {Solving Promblems on Concurrent Processors},
1995	>	Volume = {I},
1996	>	Year = 1988}
1997
1998	<	@Article{Gromacs,
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2000	<	title =        {GROMACS: A message-passing parallel molecular dynamics implementation},
2001	<	journal =      {Comp. Phys. Comm.},
2002	<	year =         1995,
2003	<	volume =       91,
2004	<	pages =        {43-56}
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1998	>	@article{Berendsen95,
1999	>	Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
2000	>	Date-Modified = {2006-02-15 10:20:47 -0500},
2001	>	Journal = {Comp. Phys. Comm.},
2002	>	Pages = {43-56},
2003	>	Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
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2005	>	Year = 1995}
2006
2007	<	@Article{Gromacs3,
2008	<	author =       {E. Lindahl and B. Hess and D. van~der~Spoel},
2009	<	title =        {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
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2011	<	year =         2001,
2012	<	volume =       7,
2013	<	pages =        {306-317}
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2007	>	@article{Lindahl01,
2008	>	Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
2009	>	Date-Modified = {2006-02-15 10:25:51 -0500},
2010	>	Journal = {J. Mol. Mod.},
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2040	>	Title = {The Missing Term in Effective Pair Potentials},
2041	>	Volume = 91,
2042	>	Year = 1987}
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2044	+	@incollection{Berendsen81,
2045	+	Address = {Dordrecht},
2046	+	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
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2259	<	title =        {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
2260	<	journal =      jcp,
2261	<	year =         1984,
2262	<	volume =       81,
2263	<	number =       7,
2449	<	pages =        {3188-3193}
2450	<	}
2257	>	@article{Hermens88,
2258	>	Author = {J. Hermans and A. Pathiaseril and A. Anderson},
2259	>	Journal = jacs,
2260	>	Pages = {5982-5986},
2261	>	Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
2262	>	Volume = 110,
2263	>	Year = 1988}
2264
2265	<	@Article{Hermens88,
2266	<	author =       {J. Hermans and A. Pathiaseril and A. Anderson},
2267	<	title =        {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
2268	<	journal =      jacs,
2269	<	year =         1988,
2270	<	volume =       110,
2271	<	pages =        {5982-5986}
2272	<	}
2265	>	@article{Meijer90,
2266	>	Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2267	>	Journal = jcp,
2268	>	Number = 12,
2269	>	Pages = {7570-7575},
2270	>	Title = {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
2271	>	Volume = 92,
2272	>	Year = 1990}
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2275	<	author =       {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2276	<	title =        {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
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2279	<	volume =       92,
2280	<	number =       12,
2468	<	pages =        {7570-7575}
2469	<	}
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2275	>	Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
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2288	<	pages =        {666-669}
2289	<	}
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2285	>	Number = 4,
2286	>	Pages = {1545-1557},
2287	>	Title = {Improved simulation of liquid water by molecular dynamics},
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2290
2291	<	@Article{Stillinger74,
2292	<	author =       {F.~H. Stillinger and A. Rahman},
2293	<	title =        {Improved simulation of liquid water by molecular dynamics},
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2295	<	year =         1974,
2296	<	volume =       60,
2297	<	number =       4,
2298	<	pages =        {1545-1557}
2488	<	}
2291	>	@article{Caldwell95,
2292	>	Author = {J.~W. Caldwell and P.~A. Kollman},
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2294	>	Number = 16,
2295	>	Pages = {6208-6219},
2296	>	Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
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2301	<	author =       {J.~W. Caldwell and P.~A. Kollman},
2302	<	title =        {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2303	<	journal =      jpc,
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2305	<	volume =       99,
2306	<	number =       16,
2307	<	pages =        {6208-6219}
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2302	>	Date-Modified = {2006-02-15 10:34:30 -0500},
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2304	>	Number = 6,
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2315	<	volume =       112,
2316	<	number =       6,
2317	<	pages =        {2843-2848}
2508	<	}
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2511	<	author =       {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
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2311	>	Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2312	>	Journal = prl,
2313	>	Number = 14,
2314	>	Pages = 146102,
2315	>	Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2316	>	Volume = 92,
2317	>	Year = 2004}

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