trunk/multipole/multipole.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Dan Gezelter at 2014-07-17 13:44:54 -0400 


%% Saved with string encoding Unicode (UTF-8) 


@string{cpl = {Chem. Phys. Lett.}}

@string{jcp = {J. Chem. Phys.}}

@string{jctc = {J. Chem. Theory Comput.}}

@string{jpcb = {J. Phys. Chem. B}}

@string{jpcc = {J. Phys. Chem. C}}

@string{mp = {Mol. Phys.}}


@book{Allen:1989fp,
        Abstract = {{Computer simulation is an essential tool in studying the chemistry and physics of liquids.  Simulations allow us to develop models and to test them against experimental data. They can be used to evaluate approximate theories of liquids, and to provide detailed information on the structure and dynamics of model liquids at the molecular level. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods.    The first four chapters describe these methods in detail, and provide the essential background in intermolecular forces and statistical mechanics.  Chapters 5 and 6 emphasize the practical aspects of writing efficient programs and analysing the simulation results.  The remaining chapters cover advanced techniques, non-equilibrium methods, Brownian dynamics, quantum simulations, and some important applications.  FORTRAN code is presented in the text.}},
        Author = {Allen, M. P. and Tildesley, D. J.},
        Citeulike-Article-Id = {1820925},
        Citeulike-Linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/0198556454},
        Citeulike-Linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&amp;path=ASIN/0198556454},
        Citeulike-Linkout-10 = {http://www.worldcat.org/oclc/20281700},
        Citeulike-Linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&amp;path=ASIN/0198556454},
        Citeulike-Linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0198556454},
        Citeulike-Linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0198556454/citeulike00-21},
        Citeulike-Linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0198556454},
        Citeulike-Linkout-6 = {http://www.worldcat.org/isbn/0198556454},
        Citeulike-Linkout-7 = {http://books.google.com/books?vid=ISBN0198556454},
        Citeulike-Linkout-8 = {http://www.amazon.com/gp/search?keywords=0198556454\&index=books\&linkCode=qs},
        Citeulike-Linkout-9 = {http://www.librarything.com/isbn/0198556454},
        Date-Added = {2014-07-17 17:43:42 +0000},
        Date-Modified = {2014-07-17 17:43:42 +0000},
        Day = {29},
        Edition = {Reprint},
        Howpublished = {Paperback},
        Isbn = {0198556454},
        Keywords = {computer\_simulation\_of\_liquids, dynamics, liquids, molecular, simulations},
        Month = jun,
        Posted-At = {2009-09-21 01:53:35},
        Priority = {2},
        Publisher = {Oxford University Press, USA},
        Series = {Oxford science publications},
        Title = {{Computer Simulation of Liquids}},
        Url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0198556454},
        Year = {1989},
        Bdsk-Url-1 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20%5C&path=ASIN/0198556454}}

@article{Neumann:1983mz,
        Author = {Neumann, Martin},
        Date-Added = {2014-07-17 16:58:07 +0000},
        Date-Modified = {2014-07-17 17:00:43 +0000},
        Doi = {10.1080/00268978300102721},
        Journal = {Molecular Physics},
        Number = {4},
        Pages = {841-858},
        Title = {Dipole moment fluctuation formulas in computer simulations of polar systems},
        Volume = {50},
        Year = {1983},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268978300102721},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268978300102721}}

@article{Adams:1981fr,
        Author = {Adams, D.J. and Adams, E.M.},
        Date-Added = {2014-07-17 16:54:22 +0000},
        Date-Modified = {2014-07-17 17:01:16 +0000},
        Doi = {10.1080/00268978100100701},
        Journal = {Molecular Physics},
        Number = {4},
        Pages = {907-926},
        Title = {Static dielectric properties of the Stockmayer fluid from computer simulation},
        Volume = {42},
        Year = {1981},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268978100100701},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268978100100701}}

@article{Adams:1980rt,
        Author = {Adams, D.J.},
        Date-Added = {2014-07-17 16:53:50 +0000},
        Date-Modified = {2014-07-17 17:01:08 +0000},
        Doi = {10.1080/00268978000102261},
        Journal = {Molecular Physics},
        Number = {5},
        Pages = {1261-1271},
        Title = {Computer simulation of highly polar liquids: The hard sphere plus point dipole potential},
        Volume = {40},
        Year = {1980},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268978000102261},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268978000102261}}

@article{Neumann:1983yq,
        Author = {M. Neumann and O. Steinhauser},
        Date-Added = {2014-07-17 16:52:21 +0000},
        Date-Modified = {2014-07-17 17:00:52 +0000},
        Doi = {http://dx.doi.org/10.1016/0009-2614(83)80585-5},
        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Number = {4--5},
        Pages = {417 - 422},
        Title = {On the calculation of the dielectric constant using the Ewald-Kornfeld tensor},
        Volume = {95},
        Year = {1983},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0009261483805855},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/0009-2614(83)80585-5}}

@article{Price:1984fk,
        Author = {Price, S.L. and Stone, A.J. and Alderton, M.},
        Date-Added = {2013-12-28 17:30:24 +0000},
        Date-Modified = {2013-12-28 17:30:33 +0000},
        Doi = {10.1080/00268978400101721},
        Journal = mp,
        Number = {4},
        Pages = {987-1001},
        Title = {Explicit formulae for the electrostatic energy, forces and torques between a pair of molecules of arbitrary symmetry},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/00268978400101721},
        Volume = {52},
        Year = {1984},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268978400101721},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268978400101721}}

@article{Allen:2006fk,
        Author = {Allen, Michael P. and Germano, Guido},
        Date-Added = {2013-12-28 17:29:00 +0000},
        Date-Modified = {2013-12-28 17:29:00 +0000},
        Doi = {10.1080/00268970601075238},
        Journal = mp,
        Number = {20-21},
        Pages = {3225-3235},
        Title = {Expressions for forces and torques in molecular simulations using rigid bodies},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/00268970601075238},
        Volume = {104},
        Year = {2006},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268970601075238},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268970601075238}}

@article{Fukuda:2013qv,
        Author = {Fukuda, Ikuo},
        Date-Added = {2013-12-27 15:45:02 +0000},
        Date-Modified = {2013-12-27 15:45:02 +0000},
        Doi = {http://dx.doi.org/10.1063/1.4827055},
        Eid = 174107,
        Journal = jcp,
        Number = {17},
        Pages = {-},
        Title = {Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/139/17/10.1063/1.4827055},
        Volume = {139},
        Year = {2013},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/139/17/10.1063/1.4827055},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4827055}}

@article{Fukuda:2012yu,
        Author = {Fukuda, Ikuo and Kamiya, Narutoshi and Yonezawa, Yasushige and Nakamura, Haruki},
        Date-Added = {2013-12-27 15:42:57 +0000},
        Date-Modified = {2013-12-27 15:42:57 +0000},
        Doi = {http://dx.doi.org/10.1063/1.4739789},
        Eid = 054314,
        Journal = jcp,
        Number = {5},
        Pages = {-},
        Title = {Simple and accurate scheme to compute electrostatic interaction: Zero-dipole summation technique for molecular system and application to bulk water},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/137/5/10.1063/1.4739789},
        Volume = {137},
        Year = {2012},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/137/5/10.1063/1.4739789},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4739789}}

@article{Fukuda:2011jk,
        Author = {Fukuda, Ikuo and Yonezawa, Yasushige and Nakamura, Haruki},
        Date-Added = {2013-12-27 15:42:11 +0000},
        Date-Modified = {2013-12-27 15:43:08 +0000},
        Doi = {http://dx.doi.org/10.1063/1.3582791},
        Eid = 164107,
        Journal = jcp,
        Number = {16},
        Pages = {-},
        Title = {Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/134/16/10.1063/1.3582791},
        Volume = {134},
        Year = {2011},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/134/16/10.1063/1.3582791},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3582791}}

@article{LT,
        Author = {Luttinger, J. M. and Tisza, L.},
        Date-Added = {2013-12-06 18:38:44 +0000},
        Date-Modified = {2013-12-06 18:38:47 +0000},
        Doi = {10.1103/PhysRev.70.954},
        Issue = {11-12},
        Journal = {Phys. Rev.},
        Month = {Dec},
        Pages = {954--964},
        Publisher = {American Physical Society},
        Title = {Theory of Dipole Interaction in Crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRev.70.954},
        Volume = {70},
        Year = {1946},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.70.954},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.70.954}}

@article{LT2,
        Author = {Luttinger, J. M. and Tisza, Laszo},
        Date-Added = {2013-12-06 18:38:17 +0000},
        Date-Modified = {2013-12-06 18:38:20 +0000},
        Doi = {10.1103/PhysRev.72.257},
        Issue = {3},
        Journal = {Phys. Rev.},
        Month = {Aug},
        Pages = {257--257},
        Publisher = {American Physical Society},
        Title = {Errata: Theory of Dipole Interaction in Crystals [Phys. Rev. 70, 954 (1946)]},
        Url = {http://link.aps.org/doi/10.1103/PhysRev.72.257},
        Volume = {72},
        Year = {1947},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.72.257},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.72.257}}

@article{doi:10.1021/la400226g,
        Author = {Shi, Wei and Luebke, David R.},
        Date-Added = {2013-09-25 19:45:42 +0000},
        Date-Modified = {2013-09-25 19:45:42 +0000},
        Doi = {10.1021/la400226g},
        Journal = {Langmuir},
        Number = {18},
        Pages = {5563-5572},
        Title = {Enhanced Gas Absorption in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][{Tf2N}]) Confined in Silica Slit Pores: A Molecular Simulation Study},
        Volume = {29},
        Year = {2013},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/la400226g},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/la400226g}}

@article{ISI:000276097500009,
        Abstract = {{Our recently developed coarse-grain model for
   dimyristoylphosphatidylcholine (DMPC) has been improved and extended to
   dioleylphosphatidylcholine (DOPC), a more typical constituent of real
   biological membranes. Single-component DMPC and DOPC bilayers have been
   simulated using microsecond-long molecular dynamics. We investigated
   properties that are difficult or impossible to access experimentally,
   such as the pressure distribution, the spontaneous curvature and the
   diffusion pattern of individual lipid molecules. Moreover, we studied
   the dipole potential, a basic physical feature of paramount biological
   importance that cannot be currently modelled by other coarse-grain
   approaches. In fact, a complete representation of the system
   electrostatics and a realistic description of the water component make
   our method unique amongst the existing coarse-grain membrane models. The
   spontaneous permeation of water, a phenomenon out of reach of standard
   atomistic models, was also observed and quantified; this was possible
   thanks to the efficiency of our model, which is about two orders of
   magnitude less computationally expensive than atomic-level counterparts.
   Results are generally in good agreement with the literature data.
   Further model extensions and future applications are proposed.}},
        Address = {{TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND}},
        Affiliation = {{Orsi, M (Reprint Author), Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England.. Orsi, Mario; Michel, Julien; Essex, Jonathan W., Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England.}},
        Article-Number = {{155106}},
        Author = {Orsi, Mario and Michel, Julien and Essex, Jonathan W.},
        Author-Email = {{j.w.essex@soton.ac.uk}},
        Date-Added = {2013-12-06 16:46:56 +0000},
        Date-Modified = {2013-12-06 16:46:56 +0000},
        Doc-Delivery-Number = {{575VN}},
        Funding-Acknowledgement = {{Biotechnology and Biological Sciences Research Council (BBSRC)}},
        Funding-Text = {{This work has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC).}},
        Issn = {{0953-8984}},
        Journal = {J. Phys. - Cond. Matt.},
        Journal-Iso = {{J. Phys.-Condes. Matter}},
        Keywords-Plus = {{SOFT STICKY DIPOLE; LATERAL PRESSURE PROFILES; MOLECULAR-DYNAMICS SIMULATIONS; X-RAY-SCATTERING; WATER PERMEABILITY; PHOSPHOLIPID-MEMBRANES; DIOLEOYLPHOSPHATIDYLCHOLINE BILAYERS; ELECTROSTATIC PROPERTIES; TEMPERATURE-DEPENDENCE; SPONTANEOUS CURVATURE}},
        Language = {{English}},
        Number = {{15}},
        Number-Of-Cited-References = {{96}},
        Pages = {{155106}},
        Publisher = {{IOP PUBLISHING LTD}},
        Research-Areas = {{Physics}},
        Times-Cited = {{7}},
        Title = {{Coarse-grain modelling of DMPC and DOPC lipid bilayers}},
        Type = {{Article}},
        Unique-Id = {{ISI:000276097500009}},
        Volume = {{22}},
        Web-Of-Science-Categories = {{Physics, Condensed Matter}},
        Year = {{2010}},
        Bdsk-Url-1 = {http://dx.doi.org/10.1088/0953-8984/22/15/155106}}

@article{ISI:000298664400012,
        Abstract = {{A new coarse-grain model for molecular dynamics simulation of lipid
   membranes is presented. Following a simple and conventional approach,
   lipid molecules are modeled by spherical sites, each representing a
   group of several atoms. In contrast to common coarse-grain methods, two
   original (interdependent) features are here adopted. First, the main
   electrostatics are modeled explicitly by charges and dipoles, which
   interact realistically through a relative dielectric constant of unity
   (is an element of(r) = 1). Second, water molecules are represented
   individually through a new parametrization of the simple Stockmayer
   potential for polar fluids; each water molecule is therefore described
   by a single spherical site embedded with a point dipole. The force field
   is shown to accurately reproduce the main physical properties of
   single-species phospholipid bilayers comprising
   dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine
   (DOPE) in the liquid crystal phase, as well as
   distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel
   phases. Insights are presented into fundamental properties and phenomena
   that can be difficult or impossible to study with alternative
   computational or experimental methods. For example, we investigate the
   internal pressure distribution, dipole potential, lipid diffusion, and
   spontaneous self-assembly. Simulations lasting up to 1.5 microseconds
   were conducted for systems of different sizes (128, 512 and 1058
   lipids); this also allowed us to identify size-dependent artifacts that
   are expected to affect membrane simulations in general. Future
   extensions and applications are discussed, particularly in relation to
   the methodology's inherent multiscale capabilities.}},
        Address = {{185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA}},
        Affiliation = {{Orsi, M (Reprint Author), Univ Southampton, Sch Chem, Southampton, Hants, England.. Orsi, Mario; Essex, Jonathan W., Univ Southampton, Sch Chem, Southampton, Hants, England.}},
        Article-Number = {{e28637}},
        Author = {Orsi, Mario and Essex, Jonathan W.},
        Author-Email = {{orsi@soton.ac.uk}},
        Date-Added = {2013-12-06 16:46:56 +0000},
        Date-Modified = {2013-12-06 16:46:56 +0000},
        Doc-Delivery-Number = {{870JD}},
        Funding-Acknowledgement = {{United Kingdom Engineering and Physical Sciences Research Council (EPSRC)\{{[}\}EP/G050708/1]}},
        Funding-Text = {{This work was supported by the United Kingdom Engineering and Physical Sciences Research Council (EPSRC) under grant number EP/G050708/1 (http://www.epsrc.ac.uk). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.}},
        Issn = {{1932-6203}},
        Journal = {{PLOS ONE}},
        Journal-Iso = {{PLoS One}},
        Keywords-Plus = {{MOLECULAR-DYNAMICS SIMULATIONS; SIMPLE POINT-CHARGE; RANGE ELECTROSTATIC INTERACTIONS; LIQUID WATER; PHOSPHATIDYLCHOLINE BILAYERS; SPONTANEOUS CURVATURE; COMPUTER-SIMULATION; LATERAL PRESSURE; CHAIN-LENGTH; DIOLEOYLPHOSPHATIDYLCHOLINE BILAYERS}},
        Language = {{English}},
        Number = {{12}},
        Number-Of-Cited-References = {{154}},
        Pages = {{e28637}},
        Publisher = {{PUBLIC LIBRARY SCIENCE}},
        Research-Areas = {{Life Sciences \& Biomedicine - Other Topics}},
        Times-Cited = {{0}},
        Title = {{The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes}},
        Type = {{Article}},
        Unique-Id = {{ISI:000298664400012}},
        Volume = {{6}},
        Web-Of-Science-Categories = {{Biology}},
        Year = {{2011}},
        Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0028637}}

@article{schnieders:124114,
        Author = {Michael J. Schnieders and Nathan A. Baker and Pengyu Ren and Jay W. Ponder},
        Date-Added = {2013-12-06 16:46:25 +0000},
        Date-Modified = {2013-12-06 16:46:25 +0000},
        Doi = {10.1063/1.2714528},
        Eid = {124114},
        Journal = jcp,
        Keywords = {proteins; molecular biophysics; Poisson equation; Boltzmann equation; molecular moments; molecular force constants; polarisability; permittivity; molecular dynamics method; biochemistry; binding energy; molecular configurations; solvation; bioelectric phenomena},
        Number = {12},
        Numpages = {21},
        Pages = {124114},
        Publisher = {AIP},
        Title = {Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum},
        Url = {http://link.aip.org/link/?JCP/126/124114/1},
        Volume = {126},
        Year = {2007},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/126/124114/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2714528}}

@article{Ravichandran:1999fk,
        Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
        Author = {Ravichandran, S and Bagchi, B},
        Date-Added = {2013-12-06 16:46:16 +0000},
        Date-Modified = {2013-12-06 16:46:16 +0000},
        Journal = jcp,
        Pages = {7505-7511},
        Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
        Volume = 111,
        Year = 1999}

@article{Berardi98,
        Author = {R. Berardi and C. Fava and C. Zannoni},
        Date-Added = {2013-12-06 16:46:09 +0000},
        Date-Modified = {2013-12-06 16:46:09 +0000},
        Journal = Cpl,
        Pages = {8-14},
        Title = {A {G}ay-{B}erne Potential for Dissimilar Biaxial Particles},
        Volume = 297,
        Year = 1998}

@article{Cleaver96,
        Author = {Douglas J. Cleaver and Christopher M. Care and Michael P. Allen and Maureen P. Neal},
        Date-Added = {2013-12-06 16:45:58 +0000},
        Date-Modified = {2013-12-06 16:45:58 +0000},
        Journal = pre,
        Number = 1,
        Pages = {559-567},
        Title = {Extension and generalization of the {G}ay-{B}erne potential},
        Volume = 54,
        Year = 1996}

@article{Luckhurst90,
        Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
        Date-Added = {2013-12-06 16:45:52 +0000},
        Date-Modified = {2013-12-06 16:45:52 +0000},
        Journal = {Liquid Crystals},
        Pages = {451-464},
        Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the {G}ay-{B}erne model mesogen},
        Volume = 8,
        Year = 1990}

@article{Gay81,
        Author = {J.~G. Gay and B.~J. Berne},
        Date-Added = {2013-12-06 16:45:43 +0000},
        Date-Modified = {2013-12-06 16:45:43 +0000},
        Journal = jcp,
        Pages = {3316-3319},
        Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
        Volume = 74,
        Year = 1981}

@article{Berne72,
        Author = {B.~J. Berne and P. Pechukas},
        Date-Added = {2013-12-06 16:45:34 +0000},
        Date-Modified = {2013-12-06 16:45:34 +0000},
        Journal = jcp,
        Pages = {4213-4216},
        Title = {Gaussian Model Potentials for Molecular Interactions},
        Volume = 56,
        Year = 1972}

@article{Ponder:2010fk,
        Abstract = {Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.},
        Author = {Ponder, Jay W and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S and Chodera, John D and Schnieders, Michael J and Haque, Imran and Mobley, David L and Lambrecht, Daniel S and DiStasio, Jr, Robert A and Head-Gordon, Martin and Clark, Gary N I and Johnson, Margaret E and Head-Gordon, Teresa},
        Date-Added = {2013-12-06 16:45:26 +0000},
        Date-Modified = {2013-12-06 16:45:26 +0000},
        Doi = {10.1021/jp910674d},
        Journal = jpcb,
        Journal-Full = {The journal of physical chemistry. B},
        Mesh = {Alanine; Crystallography, X-Ray; Ligands; Models, Chemical; Models, Molecular; Oligopeptides; Protein Binding; Proteins; Static Electricity; Thermodynamics},
        Number = {8},
        Pages = {2549-64},
        Pmc = {PMC2918242},
        Pmid = {20136072},
        Pst = {ppublish},
        Title = {Current status of the {AMOEBA} polarizable force field},
        Volume = {114},
        Year = {2010},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp910674d}}

@article{Tan:2006fk,
        Author = {Tan, Ming-Liang and Lucan, Laurentia and Ichiye, Toshiko},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = jcp,
        Journal1 = jcp,
        Journal2 = jcp,
        Keywords = {Water; Liquid Structure; Monte Carlo Methods; Liquid Theory; Solvation; Potential Energy Functions; Lennard-Jones Potential},
        Number = {17},
        Pages = {174505--5},
        Publisher = {Aip},
        Title = {Study of Multipole Contributions to the Structure of Water Around Ions in Solution Using the Soft Sticky Dipole-Quadrupole-Octupole ($\mbox{SSDQO}$) Model of Water},
        Ty = {Jour},
        Url = {Http://Link.Aip.Org/Link/?jcp/124/174505/1},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {Http://Link.Aip.Org/Link/?jcp/124/174505/1}}

@article{Chowdhuri:2006lr,
        Author = {Chowdhuri, Snehasis and Tan, Ming-Liang and Ichiye, Toshiko},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = jcp,
        Journal1 = jcp,
        Journal2 = jcp,
        Keywords = {Water; Molecular Dynamics Method; Liquid Theory; Liquid Structure; Lennard-Jones Potential; Self-Diffusion; Permittivity},
        Number = {14},
        Pages = {144513--8},
        Publisher = {Aip},
        Title = {Dynamical Properties of the Soft Sticky Dipole-Quadrupole-Octupole Water Model: A Molecular Dynamics Study},
        Ty = {Jour},
        Url = {Http://Link.Aip.Org/Link/?jcp/125/144513/1},
        Volume = {125},
        Year = {2006},
        Bdsk-Url-1 = {Http://Link.Aip.Org/Link/?jcp/125/144513/1}}

@article{Ichiye:2006qy,
        Author = {Ichiye, Toshiko and Tan, Ming-Liang},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = jcp,
        Journal1 = jcp,
        Journal2 = jcp,
        Keywords = {Water; Liquid Theory; Monte Carlo Methods; Potential Energy Functions; Molecular Moments; Quadrupole Moments; Lennard-Jones Potential},
        Number = {13},
        Pages = {134504--10},
        Publisher = {Aip},
        Title = {Soft Sticky Dipole-Quadrupole-Octupole Potential Energy Function for Liquid Water: An Approximate Moment Expansion},
        Ty = {Jour},
        Url = {Http://Link.Aip.Org/Link/?jcp/124/134504/1},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {Http://Link.Aip.Org/Link/?jcp/124/134504/1}}

@article{Te:2010vn,
        Abstract = {The effects of water multipole moments on the aqueous solvation of ions were determined in Monte Carlo simulations using soft-sticky dipole-quadrupole-octupole (SSDQO) water. Water molecules formed linear hydrogen bonds to Cl using the new SSDQO1 parameters, similar to multi-site models. However, the dipole vector was tilted rather than parallel to the oxygen-Na(+) internuclear vector as in most multi-site model, while experiment and ab initio molecular dynamics simulations generally indicate a range of values between tilted and parallel. By varying the multipoles in SSDQO, the octupole was found to determine the orientation around Na(+). Moreover, analysis of the multipoles of more conventional models is predictive of their performance as solvents. (C) 2010 Elsevier B.V. All rights reserved.},
        Author = {Te, Jerez A. and Ichiye, Toshiko},
        Date = {OCT 29 2010},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Doi = {10.1016/j.cplett.2010.09.043},
        Isi = {WOS:000283244700007},
        Issn = {0009-2614},
        Journal = cpl,
        Number = {4-6},
        Pages = {219--225},
        Publication-Type = {J},
        Times-Cited = {1},
        Title = {Understanding structural effects of multipole moments on aqueous solvation of ions using the soft-sticky dipole-quadrupole-octupole water model},
        Volume = {499},
        Year = {2010},
        Z8 = {0},
        Z9 = {1},
        Zb = {0},
        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2010.09.043}}

@article{Te:2010ys,
        Abstract = {The soft-sticky dipole-quadrupole-octupole (SSDQO) potential energy function for a coarse-grained single-site water model has Lennard-Jones interactions and an approximate multipole expansion for the electrostatics. Here, the Lennard-Jones parameters and multipole moments of SSDQO were optimized so that the structural, thermodynamic, dynamic, and dielectric properties agreed with experimental values of liquid water at ambient conditions. Using these parameters, the temperature and pressure dependence of various properties were shown to be in good agreement with experiment, including a temperature of maximum density at similar to 260 K. This new parametrization, referred to as SSDQO1, is both computationally faster and generally more accurate over a wide range of conditions than traditional three-site water models, which demonstrates that a model with a single dipole, quadrupole, and octupole on each water molecule can reproduce the tetrahedral hydrogen bonded network of water.},
        Author = {Te, Jerez A. and Ichiye, Toshiko},
        Date = {MAR 21 2010},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Doi = {10.1063/1.3359432},
        Isi = {WOS:000275825500040},
        Issn = {0021-9606},
        Journal = jcp,
        Number = {11},
        Pages = {114511},
        Publication-Type = {J},
        Times-Cited = {4},
        Title = {Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model},
        Volume = {132},
        Year = {2010},
        Z8 = {0},
        Z9 = {4},
        Zb = {0},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3359432}}

@article{Te:2010rt,
        Abstract = {Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a 'lone-pair' orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the 'dipole' orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars. (C) 2010 Elsevier B. V. All rights reserved.},
        Author = {Te, Jerez A. and Tan, Ming-Liang and Ichiye, Toshiko},
        Date = {MAY 17 2010},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Doi = {10.1016/j.cplett.2010.04.020},
        Isi = {WOS:000277264500021},
        Issn = {0009-2614},
        Journal = cpl,
        Number = {4-6},
        Pages = {218--223},
        Publication-Type = {J},
        Times-Cited = {7},
        Title = {Solvation of glucose, trehalose, and sucrose by the soft-sticky dipole-quadrupole-octupole water model},
        Volume = {491},
        Year = {2010},
        Z8 = {1},
        Z9 = {7},
        Zb = {1},
        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2010.04.020}}

@article{Liu96,
        Author = {Y. Liu and T. Ichiye},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = Cpl,
        Pages = {334-340},
        Title = {The Static Dielectric Constant of the Soft Sticky Dipole Model of Liquid Water: {M}onte {C}arlo Simulation},
        Volume = 256,
        Year = 1996}

@article{Liu96b,
        Author = {Y. Liu and T. Ichiye},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = jpc,
        Pages = {2723-2730},
        Title = {Soft Sticky Dipole Potential for Liquid Water: \Uppercase{A} New Model},
        Volume = 100,
        Year = 1996}

@article{Chandra99,
        Author = {A. Chandra and T. Ichiye},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = jcp,
        Number = 6,
        Pages = {2701-2709},
        Title = {Dynamical Properties of the Soft Sticky Dipole Model of Water: \Uppercase{M}Olecular Dynamics Simulation},
        Volume = 111,
        Year = 1999}

@article{Tan03,
        Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
        Date-Added = {2013-12-06 16:45:00 +0000},
        Date-Modified = {2013-12-06 16:45:00 +0000},
        Journal = Cpl,
        Pages = {646-652},
        Title = {A Temperature of Maximum Density in Soft Sticky Dipole Water},
        Volume = 376,
        Year = 2003}

@article{Pasterny00,
        Author = {K. Pasterny and E. Gwozdz and A. Brodka},
        Date-Added = {2013-12-06 16:44:37 +0000},
        Date-Modified = {2013-12-06 16:44:37 +0000},
        Journal = {J. Mol. Liq.},
        Pages = {173-184},
        Title = {Properties of a Model Liquid Crystal: Polar {G}ay-{B}erne Particles},
        Volume = 85,
        Year = 2000}

@article{Berardi99,
        Author = {R. Berardi and S. Orlandi and C. Zannoni},
        Date-Added = {2013-12-06 16:44:22 +0000},
        Date-Modified = {2013-12-06 16:44:22 +0000},
        Journal = {Int. J. Mod. Phys. C},
        Pages = {477-484},
        Title = {{M}onte {C}arlo Simulations of Rod-Like {G}ay-{B}erne Mesogens With Transverse Dipoles},
        Volume = 10,
        Year = 1999}

@article{Golubkov06,
        Author = {Pavel A. Golubkov and Rengyu Ren},
        Date-Added = {2013-12-06 16:43:42 +0000},
        Date-Modified = {2013-12-06 16:43:42 +0000},
        Journal = jcp,
        Pages = 064103,
        Title = {Generalized coarse-grained model based on point multipole and {G}ay-{B}erne potentials},
        Volume = 125,
        Year = 2006}

@article{Kast03,
        Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Journal = Cpl,
        Pages = {398-404},
        Title = {Integral Equation Theory for Correcting Truncation Errors in Molecular Simulations},
        Volume = {367},
        Year = {2003}}

@article{Kastenholz:124108,
        Author = {Mika A. Kastenholz and Philippe H. Hunenberger},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {10.1063/1.2177249},
        Eid = {124108},
        Journal = jcp,
        Keywords = {Electrostatics; Molecular Biophysics; Macromolecules; Poisson Equation},
        Number = {12},
        Numpages = {12},
        Pages = {124108},
        Publisher = {Aip},
        Title = {Development of a Lattice-Sum Method Emulating Nonperiodic Boundary Conditions for the Treatment of Electrostatic Interactions in Molecular Simulations: A Continuum-Electrostatics Study},
        Url = {Http://Link.Aip.Org/Link/?jcp/124/124108/1},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {Http://Link.Aip.Org/Link/?jcp/124/124108/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2177249}}

@article{Beckd.A.C._Bi0486381,
        Affiliation = {Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610, And Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610},
        Author = {Beck, D.A.C. And Armen, R.S. And Daggett, V.},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Issn = {0006-2960},
        Journal = {Biochemistry},
        Number = {2},
        Pages = {609-616},
        Title = {Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides},
        Url = {Http://Pubs3.Acs.Org/Acs/Journals/Doilookup?In_Doi=10.1021/Bi0486381},
        Volume = {44},
        Year = {2005},
        Bdsk-Url-1 = {Http://Pubs3.Acs.Org/Acs/Journals/Doilookup?In_Doi=10.1021/Bi0486381}}

@unpublished{Fennell07,
        Author = {Christopher~J. Fennell and J.~Daniel Gezelter},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Note = {In Preparation},
        Rating = {5},
        Read = {Yes},
        Title = {Pairwise Alternatives to the {E}Wald Sum: Applications and Extension to Point Multipoles},
        Year = {2007}}

@article{Fennell:2006zl,
        Author = {Fennell, Christopher J. and Gezelter, J. Daniel},
        Doi = {http://dx.doi.org/10.1063/1.2206581},
        Eid = 234104,
        Journal = jcp,
        Number = {23},
        Pages = {-},
        Title = {Is the {E}wald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2206581}}

@article{Chen:2004du,
        Abstract = {Structural and thermodynamic properties of ionic fluids are related to those of a simpler "mimic" system with short ranged intermolecular interactions in a spatially varying effective field by use of local molecular field (LMF) theory, already successfully applied to nonuniform simple fluids. By consistently using the LMF approximation to describe only the slowly varying part of the Coulomb interaction, which we view as arising from a rigid Gaussian charge distribution with an appropriately chosen width a, exceptionally accurate results can be found. In this paper we study a uniform system of charged hard spheres in a uniform neutralizing background, where these ideas can be presented in their simplest form. At low densities the LMF theory reduces to a generalized version of the Poisson-Boltzmann approximation, but the predicted structure factor satisfies the exact Stillinger-Lovett moment conditions, and with optimal choice of or the lowest order approximation remains accurate for much stronger couplings. At high density and strong couplings the pair correlation function in the uniform mimic system with short ranged interactions is very similar to that of the full ionic system. A simple analytic formula can then describe the difference in internal energy between the ionic system and the associated mimic system.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        Author = {Chen, YG and Kaur, C and Weeks, JD},
        Date = {DEC 23 2004},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1021/jp0469261},
        Journal = jpcb,
        Pages = {19874-19884},
        Publisher = {AMER CHEMICAL SOC},
        Timescited = {5},
        Title = {Connecting systems with short and long ranged interactions: Local molecular field theory for ionic fluids},
        Volume = {108},
        Year = {2004},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0469261}}

@article{Chen:2006ii,
        Abstract = {Strong, short-ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA and lead to the formation of ion pairs in dilute ionic solutions. However, the long range of the Coulomb interactions impedes the development of a simple local picture. We address this general problem by mapping the properties of a nonuniform system with Coulomb interactions onto those of a simpler system with short-ranged intermolecular interactions in an effective external field that accounts for the averaged effects of appropriately chosen long-ranged and slowly varying components of the Coulomb interactions. The remaining short-ranged components combine with the other molecular core interactions and strongly affect pair correlations in dense or strongly coupled systems. We show that pair correlation functions in the effective short-ranged system closely resemble those in the uniform primitive model of ionic solutions and illustrate the formation of ion pairs and clusters at low densities. The theory accurately describes detailed features of the effective attraction between two equally charged walls at strong coupling and intermediate separations of the walls. Analytical results for the minimal coupling strength needed to get any attraction and for the separation at which the attractive force is a maximum are presented.},
        Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
        Author = {Chen, YG and Weeks, JD},
        Date = {MAY 16 2006},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1073/pnas.0600282103},
        Journal = pnas,
        Keywords = {effective short-ranged model; ion pairing; mean field theory; Poission-Boltzmann},
        Pages = {7560-7565},
        Publisher = {NATL ACAD SCIENCES},
        Timescited = {4},
        Title = {Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions},
        Volume = {103},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0600282103}}

@article{Rodgers:2006nw,
        Author = {Rodgers, Jocelyn M. and Kaur, Charanbir and Chen, Yng-Gwei and Weeks, John D.},
        Doi = {10.1103/PhysRevLett.97.097801},
        Issue = {9},
        Journal = {Phys. Rev. Lett.},
        Month = {Aug},
        Numpages = {4},
        Pages = {097801},
        Publisher = {American Physical Society},
        Title = {Attraction Between Like-Charged Walls: Short-Ranged Simulations Using Local Molecular Field Theory},
        Url = {http://link.aps.org/doi/10.1103/PhysRevLett.97.097801},
        Volume = {97},
        Year = {2006},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.97.097801},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.97.097801}}

@article{Denesyuk:2008ez,
        Abstract = {We propose a simplified version of local molecular field (LMF) theory to treat Coulomb interactions in simulations of ionic fluids. LMF theory relies on splitting the Coulomb potential into a short-ranged part that combines with other short-ranged core interactions and is simulated explicitly. The averaged effects of the remaining long-ranged part are taken into account through a self-consistently determined effective external field. The theory contains an adjustable length parameter sigma that specifies the cutoff distance for the short-ranged interaction. This can be chosen to minimize the errors resulting from the mean-field treatment of the complementary long-ranged part. Here we suggest that in many cases an accurate approximation to the effective field can be obtained directly from the equilibrium charge density given by the Debye theory of screening, thus eliminating the need for a self-consistent treatment. In the limit sigma -> 0, this assumption reduces to the classical Debye approximation. We examine the numerical performance of this approximation for a simple model of a symmetric ionic mixture. Our results for thermodynamic and structural properties of uniform ionic mixtures agree well with similar results of Ewald simulations of the full ionic system. In addition, we have used the simplified theory in a grand-canonical simulation of a nonuniform ionic mixture where an ion has been fixed at the origin. Simulations using short-ranged truncations of the Coulomb interactions alone do not satisfy the exact condition of complete screening of the fixed ion, but this condition is recovered when the effective field is taken into account. We argue that this simplified approach can also be used in the simulations of more complex nonuniform systems. (c) 2008 American Institute of Physics.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Denesyuk, Natalia A. and Weeks, John D.},
        Date = {MAR 28 2008},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Journal = jcp,
        Publisher = {AMER INST PHYSICS},
        Timescited = {0},
        Title = {A new approach for efficient simulation of {C}oulomb interactions in ionic fluids},
        Volume = {128},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/124109}}

@article{Izvekov:2008wo,
        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.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        Author = {Izvekov, Sergei and Swanson, Jessica M. J. and Voth, Gregory A.},
        Date = {APR 17 2008},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1021/jp710339n},
        Journal = jpcb,
        Pages = {4711-4724},
        Publisher = {AMER CHEMICAL SOC},
        Timescited = {0},
        Title = {Coarse-graining in interaction space: A systematic approach for replacing long-range electrostatics with short-range Potentials},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp710339n}}

@article{Essmann95,
        Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Journal = jcp,
        Number = {19},
        Pages = {8577-8593},
        Title = {A Smooth Particle Mesh {E}Wald Method},
        Volume = {103},
        Year = {1995}}

@article{Hansen:2012uq,
        Abstract = {In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen - McDonald molten salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful measures for the convergence of the Wolf method to the Ewald summation method. The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J.; Gezelter, J. D. J. Chem. Phys. 2006, 124, 234104]. Besides its conceptual simplicity, the SF approximation implies a speed-up of a factor of 2-3 compared to the Wolf method. We conclude that for the systems studied, whenever the Wolf method gives accurate results, it may be replaced by the simpler and faster SF method.},
        Author = {Hansen, J. S. and Schroder, Thomas B. and Dyre, Jeppe C.},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1021/jp300750g},
        Isi = {000304073400020},
        Isi-Recid = {207010133},
        Isi-Ref-Recids = {72962882 142380147 57439299 83735414 119639410 161852835 150775183 97926727 150775186 99223832 27261335 192524727 54857943 201842856 174212314 175369396 93668462 157079712 103281654 37628375 52514734 154374715 112164717 175257924 197625707 195348863 148601812 180436670 19981743 109783788 142948953 148252911 143983050 150547923 126854662},
        Iso-Source-Abbreviation = {J Phys Chem B},
        Journal = jpcb,
        Pages = {5738--5743},
        Times-Cited = {7},
        Title = {Simplistic {C}oulomb Forces in Molecular Dynamics: Comparing the {W}olf and Shifted-Force Approximations},
        Volume = {116},
        Year = {2012},
        Bdsk-Url-1 = {http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/000304073400020}}

@article{McCann:2013fk,
        Abstract = {Room temperature ionic liquid calculations require extensive sampling due to the large degree of localized structuring in the liquid phase relative to conventional solutions. Consequently, a large amount of computer time is required for the convergence of solvent properties, much of which is spent evaluating long-range electrostatics via Ewald summations. The damped Coulomb potential and cutoff-neutralized method of Wolf et al. (J. Chem. Phys. 1999, 110, 8254) provides the framework for an accurate, linear-scaling alternative to Ewald in the ionic liquid simulations. The method has been the subject of multiple modifications for improved accuracy, including the damped Coulombic potential of Zahn et al. (J. Phys. Chem. B 2002, 106, 10725), the damped shifted force method of Fennell and Gezelter (J. Chem. Phys. 2006, 124, 234104), and the shifted force gradient of Kale and Herzfeld (J. Chem. Theory Comput. 2011, 7, 3620). These pairwise electrostatic interaction alternatives along with the CHARMM shifted force potential and a new method proposed herein, the shifted force third derivative (SF3), have been examined on 59 unique ionic liquid combinations of 1-alkyl-3-methylimidazolium [RMIM] (R = M (methyl), E (ethyl), B (butyl), H (hexyl), and 0 (octyl)) and N-alkylpyridinium [RPyr] cations, along with Cl-, PF6-, BF4-, NO3-, AlCl4-, Al2Cl7-, and TfO- anions. Monte Carlo simulations utilizing our custom OPLS-AA ionic liquid force field and employing the pairwise alternatives with multiple cutoff distances and electrostatic damping values are compared to the energetics from full Ewald sums.},
        Author = {McCann, Billy W. and Acevedo, Orlando},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1021/ct300961e},
        Isi = {000315018300011},
        Isi-Recid = {214392485},
        Isi-Ref-Recids = {154491573 90523733 49016001 57439299 83735414 107505781 93573488 5312 150775186 202026046 82357785 197771964 207010133 147081990 62014150 201842856 73951877 93668462 66902949 157079712 208274411 179713333 81618253 188839781 194999865 203199695 160750185 159180330 87659780 96245693 180436670 111370971 109783788 208231779 126854662},
        Iso-Source-Abbreviation = {J Chem Theory Comput},
        Journal = jctc,
        Pages = {944--950},
        Times-Cited = {0},
        Title = {Pairwise Alternatives to {E}wald Summation for Calculating Long-Range Electrostatics in Ionic Liquids},
        Volume = {9},
        Year = {2013},
        Bdsk-Url-1 = {http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/000315018300011}}

@article{kannam:094701,
        Author = {Sridhar Kumar Kannam and B. D. Todd and J. S. Hansen and Peter J. Daivis},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {10.1063/1.4793396},
        Eid = {094701},
        Journal = jcp,
        Keywords = {carbon nanotubes; flow simulation; molecular dynamics method; nonequilibrium flow; pipe flow; slip flow; water},
        Number = {9},
        Numpages = {9},
        Pages = {094701},
        Publisher = {AIP},
        Title = {How fast does water flow in carbon nanotubes?},
        Url = {http://link.aip.org/link/?JCP/138/094701/1},
        Volume = {138},
        Year = {2013},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/138/094701/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4793396}}

@article{Forrest:2012ly,
        Annote = {doi: 10.1021/jp306084t},
        Author = {Forrest, Katherine A. and Pham, Tony and McLaughlin, Keith and Belof, Jonathan L. and Stern, Abraham C. and Zaworotko, Michael J. and Space, Brian},
        Da = {2012/07/26},
        Date = {2012/06/25},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {10.1021/jp306084t},
        Isbn = {1932-7447},
        Journal = jpcc,
        M3 = {doi: 10.1021/jp306084t},
        Number = {29},
        Pages = {15538--15549},
        Publisher = {American Chemical Society},
        Title = {Simulation of the Mechanism of Gas Sorption in a Metal--Organic Framework with Open Metal Sites: Molecular Hydrogen in PCN-61},
        Ty = {JOUR},
        Url = {http://dx.doi.org/10.1021/jp306084t},
        Volume = {116},
        Year = {2012},
        Year1 = {2012},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp306084t}}

@article{English:2008kx,
        Abstract = {Equilibrium molecular dynamics (MD) simulations for three system sizes of fully occupied methane hydrate have been performed at around 265K to estimate the thermal conductivity using the Ewald, Lekner, reaction field, shifted-force and undamped Fennell-Gezelter methods. The TIP4P water model was used in conjunction with a fully atomistic methane potential with which it had been parameterized from quantum simulation. The thermal conductivity was evaluated by integration of the heat flux autocorrelation function (ACF) derived from the Green-Kubo formalism; this approach vas validated by estimation of the average phonon mean free path. The thermal conductivities predicted by non-periodic techniques were in reasonable agreement with the experimental results of 0.62 and 0.68W/mK, although it was found that the estimates by the non-periodic techniques were up to 25\% larger than those of Lekner and Ewald estimates, particularly for larger systems. The results for the Lekner method exhibited the least variation with respect to system size. A decomposition of the heat flux vector into its respective contributions revealed the importance of electrostatic interactions, and how different electrostatic treatments affect the contribution to the thermal conductivity.},
        Author = {English, Niall J.},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1080/00268970802360348},
        Isi = {000260831600006},
        Isi-Recid = {174576369},
        Isi-Ref-Recids = {64516210 50663994 23737594 9332 1341305 117276757 87187902 174576370 41402923 155828533 145080270 131025605 148117192 151887523 127578858 47256160 94875498 5312 150775186 104215944 42204741 54857943 94999161 96211695 110142188 156201339 98188526 49588888 110451703 67889715 60557738 77407659 69613783 74049883 109617764 174576371 133739710 134139841 10537236 82674909 56021114 50855953 108947051 39309 147081167 82575041 21885040 159301126 124373331 104464893 82217478 146694243 54509243 103065253 100979739 119616975 66867200 88193723 62875649 62232105 155715047},
        Iso-Source-Abbreviation = {Mol Phys},
        Journal = mp,
        Keywords = {thermal conductivity; methane hydrate; molecular dynamics; electrostatics; Green-Kubo},
        Pages = {1887--1898},
        Times-Cited = {13},
        Title = {Effect of electrostatics techniques on the estimation of thermal conductivity via equilibrium molecular dynamics simulation: application to methane hydrate},
        Volume = {106},
        Year = {2008},
        Bdsk-Url-1 = {http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/000260831600006}}

@article{Louden:2013ve,
        Author = {Louden, Patrick. and Schoenborn, R. and Lawrence, Christopher. P.},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Day = {15},
        Doi = {http://dx.doi.org/10.1016/j.fluid.2013.04.006},
        Isbn = {0378-3812},
        Journal = {Fluid Phase Equilibria},
        Keywords = {Water; Condensation coefficient; Molecular dynamics},
        Number = {0},
        Pages = {83--86},
        Title = {Molecular dynamics simulations of the condensation coefficient of water},
        Ty = {JOUR},
        Url = {http://www.sciencedirect.com/science/article/pii/S037838121300174X},
        Volume = {349},
        Year = {2013},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S037838121300174X},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.fluid.2013.04.006}}

@article{Tokumasu:2013zr,
        Abstract = {The lubrication phenomenon occurring by shearing a nanoscale liquid bridge was simulated using the molecular dynamics method by varying the width of the liquid bridge, and the momentum transport phenomena of the liquid bridge were analyzed. The Fennell method was used to calculate the coulombic interaction and the Lees-Edwards method was used to maintain the velocity gradient in the liquid bridge. First, to estimate the overall viscosity coefficient of the liquid bridge, the width and interfacial region of the liquid bridge were determined. The overall viscosity coefficient was then modeled by considering two contributions from the bulk and interfacial region and the momentum fluxes or viscosity coefficients in the bulk and interfacial region were obtained. The model approximately expresses the simulation results, and the viscosity of the interfacial region was determined to be between one fourth and one third of that of the bulk. In addition, the partial momentum fluxes were calculated to verify the validity of the proposed model. (C) 2012 Elsevier Ltd. All rights reserved.},
        Author = {Tokumasu, Takashi and Meurisse, Marie-Helene and Fillot, Nicolas and Vergne, Philippe},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {DOI 10.1016/j.triboint.2012.08.009},
        Isi = {000315243000002},
        Isi-Recid = {214463043},
        Isi-Ref-Recids = {214463044 157422618 123438813 114540019 64190493 191334149 128083667 162125881 163105305 119439041 110813454 109009860 214463045 130282885 79868072 123544820 123505095 175369396 111085007 116361769 114835737 21555860 123505180 121037013 118462450 151762829 171203774 124473947 134809679 112404833 115772352 132042586},
        Iso-Source-Abbreviation = {Tribol Int},
        Journal = {Tribology International},
        Keywords = {Liquid bridge; Molecular dynamics; Momentum transport},
        Pages = {10--16},
        Times-Cited = {0},
        Title = {A molecular dynamics study of a nanoscale liquid bridge under shear},
        Volume = {59},
        Year = {2013},
        Bdsk-Url-1 = {http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/000315243000002}}

@article{Ren:2011uq,
        Abstract = {An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 {\AA}. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.},
        Author = {Ren, Pengyu and Wu, Chuanjie and Ponder, Jay W},
        Date-Added = {2013-12-06 16:42:41 +0000},
        Date-Modified = {2013-12-06 16:42:41 +0000},
        Doi = {10.1021/ct200304d},
        Journal = jctc,
        Journal-Full = {Journal of chemical theory and computation},
        Number = {10},
        Pages = {3143-3161},
        Pmc = {PMC3196664},
        Pmid = {22022236},
        Pst = {ppublish},
        Title = {Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules},
        Volume = {7},
        Year = {2011},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/ct200304d}}

@article{Aguado03,
        Author = {A. Aguado and P.~A. Madden},
        Date-Added = {2013-07-10 15:18:11 +0000},
        Date-Modified = {2013-07-10 15:18:11 +0000},
        Doi = {10.1063/1.1605941},
        Journal = {J. Chem. Phys.},
        Number = {14},
        Pages = {7471-7483},
        Title = {Ewald summation of electrostatic multipole interactions up to the quadrupolar level},
        Volume = {119},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1605941}}

@article{deLeeuw80,
        Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
        Date-Added = {2013-07-10 15:18:02 +0000},
        Date-Modified = {2013-07-10 15:18:02 +0000},
        Journal = {Proc. R. Soc. London Ser. A},
        Number = {1752},
        Pages = {27-56},
        Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. \uppercase{I. L}attice Sums and Dielectric Constants},
        Volume = {373},
        Year = {1980}}

@article{Smith81,
        Author = {E.~R. Smith},
        Date-Added = {2013-07-10 15:18:02 +0000},
        Date-Modified = {2013-07-10 15:18:02 +0000},
        Journal = {Proc. R. Soc. London Ser. A},
        Pages = {475-505},
        Title = {Electrostatic Energy in Ionic Crystals},
        Volume = {375},
        Year = {1981}}

@article{Smith82,
        Author = {W. Smith},
        Date-Added = {2013-07-10 15:18:02 +0000},
        Date-Modified = {2013-07-10 15:24:21 +0000},
        Journal = {CCP5 Information Quarterly},
        Pages = {13-25},
        Title = {Point multipoles in the \uppercase{E}wald summation},
        Volume = 4,
        Year = 1982}

@article{Smith96,
        Author = {W. Smith and T. Forester},
        Date-Added = {2013-07-10 15:18:02 +0000},
        Date-Modified = {2013-07-10 15:18:02 +0000},
        Journal = {J. Molec. Graphics.},
        Number = 3,
        Pages = {136-141},
        Title = {\uppercase{DL\_POLY\_2.0: A} general-purpose parallel molecular dynamics simulation package},
        Volume = 14,
        Year = 1996}

@article{Smith98,
        Author = {W. Smith},
        Date-Added = {2013-07-10 15:18:02 +0000},
        Date-Modified = {2013-07-10 15:18:02 +0000},
        Journal = {CCP5 Information Quarterly},
        Pages = {18-30},
        Title = {Point multipoles in the \uppercase{E}wald summation (Revisited)},
        Volume = {46},
        Year = {1998}}

@article{Meineke05,
        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
        Date-Added = {2013-07-10 15:17:35 +0000},
        Date-Modified = {2013-07-10 15:17:35 +0000},
        Journal = {J. Comp. Chem.},
        Pages = {252-271},
        Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
        Volume = 26,
        Year = 2005}

@article{Fennell06,
        Author = {C.~J. Fennell and J.~D. Gezelter},
        Date-Added = {2013-07-10 15:17:31 +0000},
        Date-Modified = {2013-07-10 15:17:31 +0000},
        Doi = {10.1063/1.2206581},
        Journal = {J. Chem. Phys.},
        Number = {23},
        Pages = {234104(12)},
        Rating = {5},
        Read = {Yes},
        Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}

@article{Wolf99,
        Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
        Date-Added = {2013-07-10 15:17:24 +0000},
        Date-Modified = {2013-07-10 15:17:24 +0000},
        Journal = {J. Chem. Phys.},
        Number = {17},
        Pages = {8254-8282},
        Rating = {0},
        Read = {No},
        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
        Volume = {110},
        Year = {1999}}

@article{Zahn02,
        Author = {D. Zahn and B. Schilling and S.~M. Kast},
        Date-Added = {2013-07-10 15:17:24 +0000},
        Date-Modified = {2013-07-10 15:17:24 +0000},
        Journal = {J. Phys. Chem. B},
        Number = {41},
        Pages = {10725-10732},
        Title = {Enhancement of the \uppercase{W}olf Damped Coulomb Potential: $\mbox{S}$tatic, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
        Volume = {106},
        Year = {2002}}

@article{Ma05,
        Author = {Y. Ma and S.~H. Garofalini},
        Date-Added = {2013-07-10 15:17:24 +0000},
        Date-Modified = {2013-07-10 15:17:24 +0000},
        Journal = {Mol. Simul.},
        Number = 11,
        Pages = {739-748},
        Title = {Modified Wolf electrostatic summation: Incorporating an empirical charge overlap},
        Volume = 31,
        Year = 2005}

@article{Sauer,
        Author = {Sauer, J. A.},
        Date-Added = {2013-09-17 16:24:40 +0000},
        Date-Modified = {2013-09-17 16:24:45 +0000},
        Doi = {10.1103/PhysRev.57.142},
        Issue = {2},
        Journal = {Phys. Rev.},
        Pages = {142--146},
        Publisher = {American Physical Society},
        Title = {Magnetic Energy Constants of Dipolar Lattices},
        Url = {http://link.aps.org/doi/10.1103/PhysRev.57.142},
        Volume = {57},
        Year = {1940},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.57.142},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.57.142}}

@article{Nagai01081960,
        Abstract = {The quadrupole array for the lowest energy of quadrupole interaction in crystals is obtained by generalizing Luttinger and Tisza's theory of dipole interaction. The theory is presented for the two kinds of problems: the simplest case of quadrupole pertaining to a doubly degenerate orbital eg and the other general cases both for the cubic crystals. In the former case, the quadrupole interaction is written in terms of fictitious spins, whence we can get the solution of lowest energy classically, serving to obtain some informations of the orbital ordering in compounds with Mn3+, Cu2+ and Cr2+. In the latter cases, the five components of the quadrupole are totally effective, leading to a rather complicated problem. The classical solution is, however, easily obtained, though somewhat complicated. The quadrupole array of lowest energy in face-centered cubic lattice proves to be realized in molecular crystals N2, N2O, CO2 and CO, which is accompanied with large quadrupole but without or with small dipole moment.},
        Author = {Nagai, Ojiro and Nakamura, Tuto},
        Date-Added = {2013-09-17 16:23:13 +0000},
        Date-Modified = {2013-09-17 16:23:13 +0000},
        Doi = {10.1143/PTP.24.432},
        Journal = {Progress of Theoretical Physics},
        Number = {2},
        Pages = {432-454},
        Title = {Quadrupole Interaction in Crystals},
        Url = {http://ptp.oxfordjournals.org/content/24/2/432.abstract},
        Volume = {24},
        Year = {1960},
        Bdsk-Url-1 = {http://ptp.oxfordjournals.org/content/24/2/432.abstract},
        Bdsk-Url-2 = {http://dx.doi.org/10.1143/PTP.24.432}}

@article{Nagai01091963,
        Author = {Nagai, Ojiro and Nakamura, Tuto},
        Date-Added = {2013-09-17 16:22:11 +0000},
        Date-Modified = {2013-09-17 16:22:11 +0000},
        Doi = {10.1143/PTP.30.412a},
        Journal = {Progress of Theoretical Physics},
        Number = {3},
        Pages = {412},
        Title = {Quadrupole Interaction in Crystals},
        Url = {http://ptp.oxfordjournals.org/content/30/3/412.1.short},
        Volume = {30},
        Year = {1963},
        Bdsk-Url-1 = {http://ptp.oxfordjournals.org/content/30/3/412.1.short},
        Bdsk-Url-2 = {http://dx.doi.org/10.1143/PTP.30.412a}}
Revision:	4195
Committed:	Thu Jul 17 18:24:41 2014 UTC (9 years, 11 months ago) by gezelter
File size:	65125 byte(s)
Log Message:	Most recent version including dielectric stuff