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Revision 2575 by chrisfen, Sat Jan 28 22:42:46 2006 UTC vs.
Revision 2636 by chrisfen, Sat Mar 18 05:31:17 2006 UTC

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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 2006-03-17 18:29:44 -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 <
269 < @Article{Zwanzig88,
270 <  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{Sagui99,
49 >        Author = {C. Sagui and T.~A. Darden},
50 >        Date-Added = {2006-03-17 18:27:01 -0500},
51 >        Date-Modified = {2006-03-17 18:29:36 -0500},
52 >        Journal = {Annu. Rev. Biophys. Biomol. Struct.},
53 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Darden_electrostaticInBiomolecules_99.pdf},
54 >        Pages = {155-179},
55 >        Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
56 >        Volume = {28},
57 >        Year = {1999}}
58  
59 < @Article{Stillinger95,
60 <  author =       {F.~H. Stillinger},
61 <  title =        {A Topographic View of Supercooled Liquids and Glass
62 <                  Formation},
63 <  journal =      {Science},
64 <  year =         1995,
65 <  volume =       267,
66 <  pages =        {1935-1939}
67 < }
59 > @article{Perram88,
60 >        Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
61 >        Date-Added = {2006-03-17 13:42:04 -0500},
62 >        Date-Modified = {2006-03-17 13:59:01 -0500},
63 >        Journal = {Mol. Phys.},
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 < @InCollection{Angell85,
70 <  author =       {C.~A. Angell},
71 <  title =        {unknown},
72 <  booktitle =    {Relaxations in Complex Systems},
73 <  publisher =    {National Technical Information Service,
74 <                  U.S. Department of Commerce},
75 <  year =         1985,
76 <  editor =       {K.~Ngai and G.~B. Wright},
77 <  address =      {Springfield, VA},
297 <  pages =        1
298 < }
69 > @article{Woodcock71,
70 >        Author = {L.~V. Woodcock and K. Singer},
71 >        Date-Added = {2006-03-17 11:14:17 -0500},
72 >        Date-Modified = {2006-03-17 11:16:52 -0500},
73 >        Journal = {Trans. Faraday Soc.},
74 >        Pages = {12-30},
75 >        Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
76 >        Volume = {67},
77 >        Year = {1971}}
78  
79 < @Article{Bembenek96,
80 <  author =       {S.~D. Bembenek and B.~B. Laird},
81 <  title =        {The role of localization in glasses and supercooled liquids},
82 <  journal =      jcp,
83 <  year =         1996,
84 <  volume =       104,
85 <  pages =        5199
86 < }
79 > @article{Smith81,
80 >        Author = {E.~R. Smith},
81 >        Date-Added = {2006-03-16 13:47:17 -0500},
82 >        Date-Modified = {2006-03-16 13:48:34 -0500},
83 >        Journal = {Proc. R. Soc. London Ser. A},
84 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
85 >        Pages = {475-505},
86 >        Title = {Electrostatic Energy in Ionic Crystals},
87 >        Volume = {375},
88 >        Year = {1981}}
89  
90 < @Article{Sun97,
91 <  author =       {X. Sun and W.~H. Miller},
92 <  title =        {Semiclassical initial value representation for
93 <                  electronically nonadiabatic molecular dynamics},
94 <  journal =      jcp,
95 <  year =         1997,
96 <  volume =       106,
97 <  pages =        6346
98 < }
90 > @article{Weber00,
91 >        Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
92 >        Date-Added = {2006-03-16 09:49:22 -0500},
93 >        Date-Modified = {2006-03-16 09:51:17 -0500},
94 >        Doi = {10.1021/jp9937757},
95 >        Journal = {J. Phys. Chem. B},
96 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
97 >        Number = {15},
98 >        Pages = {3668-3675},
99 >        Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
100 >        Volume = {104},
101 >        Year = {2000}}
102  
103 < @Article{Spath96,
104 <  author =       {B.~W. Spath and W.~H. Miller},
105 <  title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
106 <                  PROBABILITIES},
107 <  journal =      jcp,
108 <  year =         1996,
109 <  volume =       104,
110 <  pages =        95
111 < }
103 > @article{Hunenberger99,
104 >        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
105 >        Date-Added = {2006-03-16 09:45:10 -0500},
106 >        Date-Modified = {2006-03-16 09:49:15 -0500},
107 >        Journal = {Biophys. Chem.},
108 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
109 >        Pages = {69-88},
110 >        Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
111 >        Volume = {78},
112 >        Year = {1999}}
113  
114 < @Book{Warshel91,
115 <  author =       {Arieh Warshel},
116 <  title =        {Computer modeling of chemical reactions in enzymes
117 <                  and solutions},
118 <  publisher =    {Wiley},
119 <  year =         1991,
120 <  address =      {New York}
121 < }
114 > @article{Petersen95,
115 >        Author = {H.~G. Petersen},
116 >        Date-Added = {2006-03-16 08:43:02 -0500},
117 >        Date-Modified = {2006-03-16 08:44:32 -0500},
118 >        Journal = {J. Chem. Phys.},
119 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
120 >        Month = {September},
121 >        Number = {9},
122 >        Pages = {3668-3679},
123 >        Title = {Accuracy and efficiency of the particle mesh Ewald method},
124 >        Volume = {103},
125 >        Year = {1995}}
126  
127 < @Article{Vuilleumier97,
128 <  author =       {Rodolphe Vuilleumier and Daniel Borgis},
129 <  title =        {Molecular Dynamics of an excess proton in water
130 <                  using a non-additive valence bond force field},
131 <  journal =      jpc,
132 <  year =         1997,
133 <  volume =       {in press}
134 < }
127 > @article{Luty95,
128 >        Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
129 >        Date-Added = {2006-03-16 08:39:13 -0500},
130 >        Date-Modified = {2006-03-16 08:41:15 -0500},
131 >        Journal = {J. Chem. Phys.},
132 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
133 >        Number = {8},
134 >        Pages = {3014-3021},
135 >        Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
136 >        Volume = {103},
137 >        Year = {1995}}
138  
139 < @Article{Kob95a,
140 <  author =       {W. Kob and H.~C. Andersen},
141 <  title =        {Testing mode-coupling theory for a supercooled
142 <                  binary Lennard-Jones mixtures: The van Hove
143 <                  corraltion function},
144 <  journal =      pre,
145 <  year =         1995,
146 <  volume =       51,
147 <  pages =        {4626-4641}
356 < }
139 > @article{Barker73,
140 >        Author = {J.~A. Barker and R.~O. Watts },
141 >        Date-Added = {2006-03-15 18:58:17 -0500},
142 >        Date-Modified = {2006-03-15 21:17:31 -0500},
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406 >        Pages = {2698-2704},
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413 >        Journal = jcp,
414 >        Number = 6,
415 >        Pages = {2705-2709},
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593 <                  Stretched-Exponential Relaxation in Low-Temperature
594 <                  Lennard-Jones Systems Using th eCage Correlation
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836 >        Pages = {2738-2743},
837 >        Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
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839 >        Year = 1996}
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847 >        Year = 1993}
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1080 >        Year = 1982}
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1094 <                  PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
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1344 >        Pages = 399,
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1835 <  journal =      jcp,
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1844 <  journal =      {J. Phys. Chem. B},
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1847 <  pages =        {4464-4470}
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1848 >        Year = 1991}
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1852 +        Journal = jpc,
1853 +        Number = 15,
1854 +        Pages = {4155-4168},
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1862 <  journal =      {J. Am. Chem. Soc.},
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1870 >        Date-Modified = {2006-02-15 10:35:07 -0500},
1871 >        Editor = {J.~H. Westbrook and R.~L. Fleischer},
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1873 >        Publisher = {John Wiley and Sons Ltd},
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1881 <  journal =      {Rev. Fr. Inform. Rech. Oper.},
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1883 <  volume =       {16-R1},
1884 <  pages =        {35-43}
1885 < }
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1879 >        Author = {S.~J. Marrink and D.~P. Teileman},
1880 >        Date-Modified = {2006-02-15 10:28:20 -0500},
1881 >        Journal = {Biophysical Journal},
1882 >        Pages = {2386-2392},
1883 >        Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
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1885 >        Year = 2002}
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1900 >        Pages = {217-227},
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2133 <  publisher =    {Materials Research Society}
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2113 >        Date-Modified = {2006-02-15 10:35:27 -0500},
2114          Journal = {Intermetallic Compounds: Principles and Practice},
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2142 >        Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
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2161 >        Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package},
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2167 <  title =        {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2168 <  journal =      {J. Comp. Chem.},
2169 <  year =         1987,
2170 <  volume =       8,
2171 <  number =       7,
2172 <  pages =        {1016-1024}
2173 < }
2165 > @article{Ponder87,
2166 >        Author = {J.~W. Ponder and F.~M. Richards},
2167 >        Date-Modified = {2006-02-15 10:13:45 -0500},
2168 >        Journal = {J. Comp. Chem.},
2169 >        Number = 7,
2170 >        Pages = {1016-1024},
2171 >        Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2172 >        Volume = 8,
2173 >        Year = 1987}
2174  
2175 < @Article{Berendsen87,
2176 <  author =       {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2177 <  title =        {The Missing Term in Effective Pair Potentials},
2178 <  journal =      jpc,
2179 <  year =         1987,
2180 <  volume =       91,
2181 <  pages =        {6269-6271}
2206 < }
2175 > @article{Berendsen87,
2176 >        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2177 >        Journal = jpc,
2178 >        Pages = {6269-6271},
2179 >        Title = {The Missing Term in Effective Pair Potentials},
2180 >        Volume = 91,
2181 >        Year = 1987}
2182  
2183 < @InCollection{Berendsen81,
2184 <  author =       {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2185 <  title =        {Simple Point Charge Water},
2186 <  booktitle =    {Intermolecular Forces},
2187 <  pages =        331,
2188 <  publisher =    {Reidel},
2189 <  year =         1981,
2190 <  editor =       {B. Pullman},
2191 <  address =      {Dordrecht}
2217 < }
2183 > @incollection{Berendsen81,
2184 >        Address = {Dordrecht},
2185 >        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2186 >        Booktitle = {Intermolecular Forces},
2187 >        Editor = {B. Pullman},
2188 >        Pages = 331,
2189 >        Publisher = {Reidel},
2190 >        Title = {Simple Point Charge Water},
2191 >        Year = 1981}
2192  
2193 + @article{Mahoney00,
2194 +        Author = {M.~W. Mahoney and W.~L. Jorgensen},
2195 +        Journal = jcp,
2196 +        Number = 20,
2197 +        Pages = {8910-8922},
2198 +        Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
2199 +        Volume = 112,
2200 +        Year = 2000}
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2202 < @Article{Mahoney00,
2203 <  author =       {M.~W. Mahoney and W.~L. Jorgensen},
2204 <  title =        {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
2205 <  journal =      jcp,
2206 <  year =         2000,
2207 <  volume =       112,
2208 <  number =       20,
2209 <  pages =        {8910-8922}
2210 < }
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2203 >        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2204 >        Date-Modified = {2006-03-05 12:37:31 -0500},
2205 >        Journal = {J. Comp. Chem.},
2206 >        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
2207 >        Pages = {252-271},
2208 >        Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2209 >        Volume = 26,
2210 >        Year = 2005}
2211  
2212 + @article{Baez95a,
2213 +        Author = {L.~A. B\`{a}ez and P. Clancy},
2214 +        Journal = mp,
2215 +        Number = 3,
2216 +        Pages = {385-396},
2217 +        Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
2218 +        Volume = 86,
2219 +        Year = 1995}
2220  
2221 < @Article{Meineke05,
2222 <  author =       {M.~A. Meineke and C.~F. Vardeman~II and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2223 <  title =        {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2224 <  journal =      {J. Comp. Chem.},
2225 <  year =         2005,
2226 <  volume =       26,
2227 <  pages =        {252-271}
2228 < }
2221 > @article{Baez95b,
2222 >        Author = {L.~A. B\`{a}ez and P. Clancy},
2223 >        Journal = jcp,
2224 >        Number = 22,
2225 >        Pages = {9744-9755},
2226 >        Title = {Phase equilibria in extended simple point charge ice-water systems},
2227 >        Volume = 103,
2228 >        Year = 1995}
2229  
2230 < @Article{Baez95a,
2231 <  author =       {L.~A. B\`{a}ez and P. Clancy},
2232 <  title =        {Calculation of free energy for molecular crystals by thermodynamic integration},
2233 <  journal =      mp,
2234 <  year =         1995,
2235 <  volume =       86,
2236 <  number =       3,
2237 <  pages =        {385-396}
2248 < }
2230 > @article{Davidson84,
2231 >        Author = {E.~R. Davidson and K. Morokuma},
2232 >        Journal = jcp,
2233 >        Number = 8,
2234 >        Pages = {3741-3742},
2235 >        Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
2236 >        Volume = 81,
2237 >        Year = 1984}
2238  
2239 < @Article{Baez95b,
2240 <  author =       {L.~A. B\`{a}ez and P. Clancy},
2241 <  title =        {Phase equilibria in extended simple point charge ice-water systems},
2242 <  journal =      jcp,
2243 <  year =         1995,
2244 <  volume =       103,
2245 <  number =       22,
2246 <  pages =        {9744-9755}
2258 < }
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2240 >        Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
2241 >        Journal = prl,
2242 >        Number = 25,
2243 >        Pages = 255701,
2244 >        Title = {Phase Diagram of Water from Computer Simulation},
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2246 >        Year = 2004}
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2248 < @Article{Davidson84,
2249 <  author =       {E.~R. Davidson and K. Morokuma},
2250 <  title =        {A proposed antiferroelectric structure for proton ordered ice Ih},
2251 <  journal =      jcp,
2252 <  year =         1984,
2253 <  volume =       81,
2254 <  number =       8,
2267 <  pages =        {3741-3742}
2268 < }
2248 > @article{Onsager36,
2249 >        Author = {L. Onsager},
2250 >        Journal = jacs,
2251 >        Pages = {1486-1493},
2252 >        Title = {Electric Moments of Molecules in Liquids},
2253 >        Volume = 58,
2254 >        Year = 1936}
2255  
2256 < @Article{Sanz04,
2257 <  author =       {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
2258 <  title =        {Phase Diagram of Water from Computer Simulation},
2259 <  journal =      prl,
2260 <  year =         2004,
2261 <  volume =       92,
2262 <  number =       25,
2277 <  pages =        255701
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2257 >        Author = {M. Matsumoto and S. Saito and I. Ohimine},
2258 >        Journal = {Nature (London)},
2259 >        Pages = {409-413},
2260 >        Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
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2262 >        Year = 2002}
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2264 < @Article{Onsager36,
2265 <  author =       {L. Onsager},
2266 <  title =        {Electric Moments of Molecules in Liquids},
2267 <  journal =      jacs,
2268 <  year =         1936,
2269 <  volume =       58,
2270 <  pages =        {1486-1493}
2271 < }
2264 > @article{Yamada02,
2265 >        Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
2266 >        Journal = prl,
2267 >        Number = 19,
2268 >        Pages = 195701,
2269 >        Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
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2271 >        Year = 2002}
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2273 < @Article{Matsumoto02,
2274 <  author =       {M. Matsumoto and S. Saito and I. Ohimine},
2275 <  title =        {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
2276 <  journal =      {Nature (London)},
2277 <  year =         2002,
2278 <  volume =       416,
2279 <  pages =        {409-413},
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2273 > @article{Wallqvist95,
2274 >        Author = {A. Wallqvist and B.~J. Berne},
2275 >        Journal = jpc,
2276 >        Pages = {2885-2892},
2277 >        Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
2278 >        Volume = 99,
2279 >        Year = 1995}
2280  
2281 < @Article{Yamada02,
2282 <  author =       {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
2283 <  title =        {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
2284 <  journal =      prl,
2285 <  year =         2002,
2286 <  volume =       88,
2287 <  number =       19,
2288 <  pages =        195701,
2306 < }
2281 > @article{Vlot99,
2282 >        Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2283 >        Journal = jcp,
2284 >        Number = 1,
2285 >        Pages = {55-61},
2286 >        Title = {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
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2288 >        Year = 1999}
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2290 < @Article{Wallqvist95,
2291 <  author =       {A. Wallqvist and B.~J. Berne},
2292 <  title =        {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
2293 <  journal =      jpc,
2294 <  year =         1995,
2295 <  volume =       99,
2296 <  pages =        {2885-2892}
2297 < }
2290 > @article{Gao00,
2291 >        Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
2292 >        Journal = jcp,
2293 >        Number = 19,
2294 >        Pages = {8534-8538},
2295 >        Title = {The melting temperature of proton-disordered hexagonal ice: A computer simulation of 4-site transferable intermolecular potential model of water},
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2300 <  author =       {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2301 <  title =        {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
2302 <  journal =      jcp,
2303 <  year =         1999,
2304 <  volume =       110,
2305 <  number =       1,
2306 <  pages =        {55-61}
2325 < }
2299 > @article{Bizid87,
2300 >        Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
2301 >        Journal = jcp,
2302 >        Number = 4,
2303 >        Pages = {2225-2230},
2304 >        Title = {Structure of high-density amorphous water. I. X-ray diffraction study},
2305 >        Volume = 87,
2306 >        Year = 1987}
2307  
2308 < @Article{Gao00,
2309 <  author =       {G.~T. Gao and X.~C. Zeng and H. Tanaka},
2310 <  title =        {The melting temperature of proton-disordered hexagonal ice: A computer simulation of 4-site transferable intermolecular potential model of water},
2311 <  journal =      jcp,
2312 <  year =         2000,
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2314 <  number =       19,
2315 <  pages =        {8534-8538}
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2309 >        Author = {J. Quintana and A.~D.~J. Haymet},
2310 >        Journal = cpl,
2311 >        Number = 3,
2312 >        Pages = {273-277},
2313 >        Title = {The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models},
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2315 >        Year = 1992}
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2317 > @article{Mezei92,
2318 >        Author = {M. Mezei},
2319 >        Journal = {J. Comput. Chem.},
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2321 >        Title = {Don't Remember},
2322 >        Volume = 13,
2323 >        Year = 1992}
2324  
2325 < @Article{Bizid87,
2326 <  author =       {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
2327 <  title =        {Structure of high-density amorphous water. I. X-ray diffraction study},
2328 <  journal =      jcp,
2329 <  year =         1987,
2330 <  volume =       87,
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2344 <  pages =        {2225-2230}
2345 < }
2325 > @article{Widom63,
2326 >        Author = {B. Widom},
2327 >        Journal = jcp,
2328 >        Pages = 2808,
2329 >        Title = {Particle insertion},
2330 >        Volume = 39,
2331 >        Year = 1963}
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2333 < @Article{Quintana92,
2334 <  author =       {J. Quintana and A.~D.~J. Haymet},
2335 <  title =        {The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models},
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2337 <  year =         1992,
2338 <  volume =       189,
2339 <  number =       3,
2340 <  pages =        {273-277}
2355 < }
2333 > @article{Clancy94,
2334 >        Author = {L.~A. B\'{a}ez and P. Clancy},
2335 >        Journal = jcp,
2336 >        Number = 11,
2337 >        Pages = {9837-9840},
2338 >        Title = {Existence of a density maximum in extended simple point charge water},
2339 >        Volume = 101,
2340 >        Year = 1994}
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2342 + @article{Jorgensen98b,
2343 +        Author = {W.~L. Jorgensen and C. Jenson},
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2345 +        Number = 10,
2346 +        Pages = {1179-1186},
2347 +        Title = {Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density},
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2352 <  author =       {M. Mezei},
2353 <  title =        {Don't Remember},
2354 <  journal =      {J. Comput. Chem.},
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2356 <  volume =       13,
2357 <  pages =        651
2358 < }
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2352 >        Author = {M.~W. Mahoney and W.~L. Jorgensen},
2353 >        Journal = jcp,
2354 >        Number = 1,
2355 >        Pages = {363-366},
2356 >        Title = {Diffusion constant of the TIP5P model of liquid water},
2357 >        Volume = 114,
2358 >        Year = 2001}
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2360 + @article{Rahman75,
2361 +        Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
2362 +        Journal = jcp,
2363 +        Number = 12,
2364 +        Pages = {5223-5230},
2365 +        Title = {Study of a central force model for liquid water by molecular dynamics},
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2367 +        Year = 1975}
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2369 < @Article{Widom63,
2370 <  author =       {B. Widom},
2371 <  title =        {Particle insertion},
2372 <  journal =      jcp,
2373 <  year =         1963,
2374 <  volume =       39,
2375 <  pages =        2808
2376 < }
2369 > @article{Spoel98,
2370 >        Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
2371 >        Date-Modified = {2006-03-05 12:38:54 -0500},
2372 >        Journal = jcp,
2373 >        Number = 24,
2374 >        Pages = {10220-10230},
2375 >        Title = {A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field},
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2380 <  author =       {L.~A. B\'{a}ez and P. Clancy},
2381 <  title =        {Existence of a density maximum in extended simple point
2382 <                  charge water},
2383 <  journal =      jcp,
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2385 <  volume =       101,
2384 <  number =       11,
2385 <  pages =        {9837-9840}
2386 < }
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2380 >        Author = {K.~R. Gallagher and K.~A. Sharp},
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2388 <  author =       {W.~L. Jorgensen and C. Jenson},
2389 <  title =        {Temperature Dependence of TIP3P, SPC, and TIP4P Water
2390 <                  from NPT Monte Carlo Simulations: Seeking Temperatures
2391 <                  of Maximum Density},
2392 <  journal =      jcc,
2393 <  year =         1998,
2394 <  volume =       19,
2396 <  number =       10,
2397 <  pages =        {1179-1186}
2398 < }
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2388 >        Author = {D. Frenkel and A.~J.~C. Ladd},
2389 >        Journal = jcp,
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2391 >        Pages = {3188-3193},
2392 >        Title = {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
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2394 >        Year = 1984}
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2397 <  author =       {M.~W. Mahoney and W.~L. Jorgensen},
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2401 <  volume =       114,
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2407 <  pages =        {363-366},
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2398 >        Journal = jacs,
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2400 >        Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
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2402 >        Year = 1988}
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2406 <  title =        {Study of a central force model for liquid water by
2407 <                  molecular dynamics},
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2411 <  number =       12,
2418 <  pages =        {5223-5230}
2419 < }
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2405 >        Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2406 >        Journal = jcp,
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2408 >        Pages = {7570-7575},
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2415 <  title =        {A systematc study of water models for molecular
2416 <                  simulation: Derivation of water models optimized for
2417 <                  use with a reaction field},
2418 <  journal =      jcp,
2419 <  year =         1998,
2428 <  volume =       108,
2429 <  number =       24,
2430 <  pages =        {10220-10230}
2431 < }
2413 > @article{Li96,
2414 >        Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
2415 >        Journal = {Science},
2416 >        Pages = {666-669},
2417 >        Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2418 >        Volume = 273,
2419 >        Year = 1996}
2420  
2421 < @Article{Gallagher03,
2422 <  author =       {K.~R. Gallagher and K.~A. Sharp},
2423 <  title =        {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
2424 <  journal =      jacs,
2425 <  year =         2003,
2426 <  volume =       125,
2427 <  pages =        9853
2428 < }
2421 > @article{Stillinger74,
2422 >        Author = {F.~H. Stillinger and A. Rahman},
2423 >        Journal = jcp,
2424 >        Number = 4,
2425 >        Pages = {1545-1557},
2426 >        Title = {Improved simulation of liquid water by molecular dynamics},
2427 >        Volume = 60,
2428 >        Year = 1974}
2429  
2430 < @Article{Frenkel84,
2431 <  author =       {D. Frenkel and A.~J.~C. Ladd},
2432 <  title =        {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
2433 <  journal =      jcp,
2434 <  year =         1984,
2435 <  volume =       81,
2436 <  number =       7,
2437 <  pages =        {3188-3193}
2450 < }
2430 > @article{Caldwell95,
2431 >        Author = {J.~W. Caldwell and P.~A. Kollman},
2432 >        Journal = jpc,
2433 >        Number = 16,
2434 >        Pages = {6208-6219},
2435 >        Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2436 >        Volume = 99,
2437 >        Year = 1995}
2438  
2439 < @Article{Hermens88,
2440 <  author =       {J. Hermans and A. Pathiaseril and A. Anderson},
2441 <  title =        {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
2442 <  journal =      jacs,
2443 <  year =         1988,
2444 <  volume =       110,
2445 <  pages =        {5982-5986}
2446 < }
2439 > @article{Urbic00,
2440 >        Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2441 >        Date-Modified = {2006-02-15 10:34:30 -0500},
2442 >        Journal = jcp,
2443 >        Number = 6,
2444 >        Pages = {2843-2848},
2445 >        Title = {A two-dimensional model of water: Therory and computer simulations},
2446 >        Volume = 112,
2447 >        Year = 2000}
2448  
2449 < @Article{Meijer90,
2450 <  author =       {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2451 <  title =        {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
2452 <  journal =      jcp,
2453 <  year =         1990,
2454 <  volume =       92,
2455 <  number =       12,
2456 <  pages =        {7570-7575}
2469 < }
2470 <
2471 < @Article{Li96,
2472 <  author =       {H. Li and R. Helling and C. Tang and N. Wingreen},
2473 <  title =        {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2474 <  journal =      {Science},
2475 <  year =         1996,
2476 <  volume =       273,
2477 <  pages =        {666-669}
2478 < }
2479 <
2480 < @Article{Stillinger74,
2481 <  author =       {F.~H. Stillinger and A. Rahman},
2482 <  title =        {Improved simulation of liquid water by molecular dynamics},
2483 <  journal =      jcp,
2484 <  year =         1974,
2485 <  volume =       60,
2486 <  number =       4,
2487 <  pages =        {1545-1557}
2488 < }
2489 <
2490 < @Article{Caldwell95,
2491 <  author =       {J.~W. Caldwell and P.~A. Kollman},
2492 <  title =        {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2493 <  journal =      jpc,
2494 <  year =         1995,
2495 <  volume =       99,
2496 <  number =       16,
2497 <  pages =        {6208-6219}
2498 < }
2499 <
2500 < @Article{Dill00,
2501 <  author =       {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2502 <  title =        {A two-dimensional model of water: Therory and computer simulations},
2503 <  journal =      jcp,
2504 <  year =         2000,
2505 <  volume =       112,
2506 <  number =       6,
2507 <  pages =        {2843-2848}
2508 < }
2509 <
2510 < @Article{Yang04,
2511 <  author =       {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2512 <  title =        {Ice Tessellation on a Hydroxylated Silica Surface},
2513 <  journal =      prl,
2514 <  year =         2004,
2515 <  volume =       92,
2516 <  number =       14,
2517 <  pages =        146102
2518 < }
2519 <
2449 > @article{Yang04,
2450 >        Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2451 >        Journal = prl,
2452 >        Number = 14,
2453 >        Pages = 146102,
2454 >        Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2455 >        Volume = 92,
2456 >        Year = 2004}

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