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Revision 4187 by gezelter, Sun Jun 15 16:25:42 2014 UTC vs.
Revision 4208 by gezelter, Fri Aug 8 15:11:49 2014 UTC

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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2014-06-06 11:37:13 -0400
5 > %% Created for Dan Gezelter at 2014-08-08 10:43:40 -0400
6  
7  
8   %% Saved with string encoding Unicode (UTF-8)
# Line 10 | Line 10
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}}
# Line 18 | Line 20
20  
21   @string{mp = {Mol. Phys.}}
22  
21 – @string{jcp = {J. Chem. Phys.}}
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},
# Line 164 | Line 199
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},
168 <        pages = {-},
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},
# Line 181 | Line 216
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},
185 <        pages={-},
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},
# Line 529 | Line 564 | year={1975},
564          Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4827055}}
565  
566   @incollection{Woodcock75,
567 < year={1975},
568 < isbn={978-1-4615-8272-4},
569 < booktitle={Advances in Molten Salt Chemistry},
570 < editor={Braunstein, J. and Mamantov, Gleb and Smith, G.P.},
571 < doi={10.1007/978-1-4615-8270-0_1},
572 < title={Molecular Dynamics Calculations on Molten Ionic Salts},
573 < url={http://dx.doi.org/10.1007/978-1-4615-8270-0_1},
574 < publisher={Springer US},
575 < author={Woodcock, L.V.},
576 < pages={1-74},
577 < language={English}
578 < }
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 {Takada94,
595 < author = {Shimada, Jiro and Kaneko, Hiroki and Takada, Toshikazu},
596 < title = {Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations},
597 < journal = {Journal of Computational Chemistry},
598 < volume = {15},
599 < number = {1},
600 < publisher = {John Wiley & Sons, Inc.},
601 < issn = {1096-987X},
602 < url = {http://dx.doi.org/10.1002/jcc.540150105},
603 < doi = {10.1002/jcc.540150105},
604 < pages = {28--43},
605 < year = {1994},
606 < }
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  
560 – @article {Takada93,
561 – author = {Shimada, Jiro and Kaneko, Hiroki and Takada, Toshikazu},
562 – title = {Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions},
563 – journal = {J. Comp. Chem.},
564 – volume = {14},
565 – number = {7},
566 – publisher = {John Wiley & Sons, Inc.},
567 – issn = {1096-987X},
568 – url = {http://dx.doi.org/10.1002/jcc.540140712},
569 – doi = {10.1002/jcc.540140712},
570 – pages = {867--878},
571 – year = {1993},
572 – }
573 –
574 –
608   @article{Gunsteren94,
609 < author = {Luty, Brock A. and Davis, Malcolm E. and Tironi, Ilario G. and Van Gunsteren, Wilfred F.},
610 < title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems},
611 < journal = {Mol. Simul.},
612 < volume = {14},
613 < number = {1},
614 < pages = {11-20},
615 < year = {1994},
616 < doi = {10.1080/08927029408022004},
617 < URL = {http://dx.doi.org/10.1080/08927029408022004},
618 < }
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 <   title = "Lattice‐sum methods for calculating electrostatic interactions in molecular simulations",
623 <   journal = jcp,
624 <   year = "1995",
625 <   volume = "103",
626 <   number = "8",
627 <   pages = "3014-3021",
628 <   url = "http://scitation.aip.org/content/aip/journal/jcp/103/8/10.1063/1.470490",
629 <   doi = "http://dx.doi.org/10.1063/1.470490"
630 < }
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 < author ="Heyes, D. M. and Barber, M. and Clarke, J. H. R.",
635 < title  ="Molecular dynamics computer simulation of surface properties of crystalline potassium chloride",
636 < journal  ="J. Chem. Soc.{,} Faraday Trans. 2",
637 < year  ="1977",
638 < volume  ="73",
639 < issue  ="7",
640 < pages  ="1485-1496",
641 < publisher  ="The Royal Society of Chemistry",
642 < doi  ="10.1039/F29777301485",
643 < url  ="http://dx.doi.org/10.1039/F29777301485",
644 < 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."}
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},
# Line 620 | Line 655 | author = {{de Leeuw}, S. W. and Perram, J. W. and Smit
655          Year = {1979}}
656  
657   @article{Smith80,
658 < author = {{de Leeuw}, S. W. and Perram, J. W. and Smith, E. R.},
659 < title = {Simulation of Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
660 < volume = {373},
661 < number = {1752},
662 < pages = {27-56},
663 < year = {1980},
664 < doi = {10.1098/rspa.1980.0135},
665 < 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.},
666 < URL = {http://rspa.royalsocietypublishing.org/content/373/1752/27.abstract},
667 < journal = {Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences}
668 < }
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},
# Line 681 | Line 717 | title = "A molecular dynamics study of a nanoscale liq
717          Year = {2013}}
718  
719   @article{Vergne13,
720 < title = "A molecular dynamics study of a nanoscale liquid bridge under shear ",
721 < journal = "Tribology International ",
722 < volume = "59",
723 < number = "0",
724 < pages = "10 - 16",
725 < year = "2013",
726 < issn = "0301-679X",
727 < doi = "http://dx.doi.org/10.1016/j.triboint.2012.08.009",
728 < url = "http://www.sciencedirect.com/science/article/pii/S0301679X12002812",
729 < author = "Takashi Tokumasu and Marie-Helene Meurisse and Nicolas Fillot and Philippe Vergne",
730 < keywords = "Liquid bridge",
731 < keywords = "Molecular dynamics",
732 < keywords = "Momentum transport "
697 < }
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  
699 –
734   @article{Ren06,
735          Author = {Golubkov, Pavel A and Ren, Pengyu},
736          Journal = jcp,
# Line 769 | Line 803 | keywords = "Momentum transport "
803  
804   @article{Lacman65,
805          Author = {Lacman, R.},
806 <  title={Adsorption et croissance cristalline: Nancy, 6-12 Juin 1965},
773 <  journal={Colloq. Int. CNRS},
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}
777 < }
810 >        Year = {1965}}
811  
779 –
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},
# Line 788 | Line 820 | author = {Fisher, Ronald},
820          Year = {2014}}
821  
822   @article{fisher53,
823 < author = {Fisher, Ronald},
824 < title = {Dispersion on a Sphere},
825 < volume = {217},
826 < number = {1130},
827 < pages = {295-305},
828 < year = {1953},
829 < doi = {10.1098/rspa.1953.0064},
830 < 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.},
831 < URL = {http://rspa.royalsocietypublishing.org/content/217/1130/295.abstract},
832 < journal = {Proc. R. Soc. Lond. A}
833 < }
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 < title = "{Automated conformational analysis from crystallographic data. 1. A symmetry-modified single-linkage clustering algorithm for three-dimensional pattern recognition}",
839 < journal = "Acta Crystallographica Section B",
840 < year = "1991",
841 < volume = "47",
842 < number = "1",
843 < pages = "29--40",
844 < month = "Feb",
845 < doi = {10.1107/S0108768190010357},
846 < url = {http://dx.doi.org/10.1107/S0108768190010357},
847 < }
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}}
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}}
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}}
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}
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}}
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}}
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}}
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}}
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}}
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}}
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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}}
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}}
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.},
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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}}
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.},
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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}}
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}}
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}}
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}}
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}
998 <
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}

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