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\@writefile{toc}{\contentsline {title}{Real space alternatives to the Ewald Sum. II. performance in condensed phase simulations}{1}{}} |
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\@writefile{toc}{\contentsline {abstract}{Abstract}{1}{}} |
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\@writefile{toc}{\contentsline {section}{\numberline {I}Introduction}{1}{}} |
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\@writefile{toc}{\contentsline {subsection}{\numberline {A}Real-space methods}{1}{}} |
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\citation{Wolf99} |
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\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces NaCl crystal showing (a) breaking of the charge ordering in the direct spherical truncation, and (b) complete $(NaCl)_{4}$ molecule interacting with the central ion. }}{2}{}} |
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\@writefile{toc}{\contentsline {subsection}{\numberline {B}Damping function}{2}{}} |
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\@writefile{toc}{\contentsline {subsection}{\numberline {A}Configurational energy differences}{5}{}} |
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\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces The correlation coefficient and regression slope of configurational energy differences for a given method with compared with the reference Ewald method. The value of result equal to 1(dashed line) indicates energy difference is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 $A^o$ = circle, 12 $A^o$ = square 15 $A^o$ = inverted triangle)}}{5}{}} |
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\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces The correlation coefficient and regression slope of the magnitude of the force for a given method with compared to the reference Ewald method. The value of result equal to 1(dashed line) indicates, the magnitude of the force from a method is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 $A^o$ = circle, 12 $A^o$ = square 15 $A^o$ = inverted triangle). }}{6}{}} |
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\@writefile{toc}{\contentsline {subsection}{\numberline {C}Directionality of the force and torque vectors}{6}{}} |
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\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces The correlation coefficient and regression slope of the magnitude of the torque for a given method with compared to the reference Ewald method. The value of result equal to 1(dashed line) indicates, the magnitude of the force from a method is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 $A^o$ = circle, 12 $A^o$ = square 15 $A^o$ = inverted triangle).}}{6}{}} |
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\@writefile{toc}{\contentsline {subsection}{\numberline {D}Total energy conservation}{7}{}} |
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\@writefile{toc}{\contentsline {section}{\numberline {V}CONCLUSION}{7}{}} |
| 82 |
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces The circular variance of the data sets of the direction of the force and torque vectors obtained from a given method about reference Ewald method. The result equal to 0 (dashed line) indicates direction of the vectors are indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 $A^o$ = circle, 12 $A^o$ = square 15 $A^o$ = inverted triangle)}}{7}{}} |
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\bibcite{Woodcock86}{{1}{1986}{{Clarke, Smith,\ and\ Woodcock}}{{}}} |
| 85 |
\bibcite{Woodcock75}{{2}{1975}{{Woodcock}}{{}}} |
| 86 |
\bibcite{Wolf99}{{3}{1999}{{Wolf\ \emph {et~al.}}}{{Wolf, Keblinski, Phillpot,\ and\ Eggebrecht}}} |
| 87 |
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| 89 |
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| 90 |
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| 91 |
\bibcite{Pedersen93}{{8}{1993}{{Darden, York,\ and\ Pedersen}}{{}}} |
| 92 |
\bibcite{Pedersen95}{{9}{1995}{{Essmann\ \emph {et~al.}}}{{Essmann, Perera, Berkowitz, Darden, Lee,\ and\ Pedersen}}} |
| 93 |
\bibcite{Gezelter06}{{10}{2006}{{Fennell\ and\ Gezelter}}{{}}} |
| 94 |
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\bibcite{Clarke77}{{12}{1977}{{Heyes, Barber,\ and\ Clarke}}{{}}} |
| 96 |
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| 97 |
\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces The plot showing (a) standard deviation, and (b) total energy drift in the total energy conservation plot for different values of the damping alpha for different cut off methods. }}{8}{}} |
| 98 |
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| 99 |
\bibcite{Perram79}{{13}{1979}{{De~Leeuw\ and\ Perram}}{{}}} |
| 100 |
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| 104 |
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| 105 |
\bibcite{Zahn02}{{19}{2002}{{Zahn, Schilling,\ and\ Kast}}{{}}} |
| 106 |
\bibcite{Luebke13}{{20}{2013}{{Shi\ and\ Luebke}}{{}}} |
| 107 |
\bibcite{Daivis13}{{21}{2012}{{Kannam\ \emph {et~al.}}}{{Kannam, Todd, Hansen,\ and\ Daivis}}} |
| 108 |
\bibcite{Acevedo13}{{22}{2013}{{McCann\ and\ Acevedo}}{{}}} |
| 109 |
\bibcite{Space12}{{23}{2012}{{Forrest\ \emph {et~al.}}}{{Forrest, Pham, McLaughlin, Belof, Stern, Zaworotko,\ and\ Space}}} |
| 110 |
\bibcite{English08}{{24}{2008}{{English}}{{}}} |
| 111 |
\bibcite{Lawrence13}{{25}{2013}{{Louden, Schoenborn,\ and\ Lawrence}}{{}}} |
| 112 |
\bibcite{Vergne13}{{26}{2013}{{Tokumasu\ \emph {et~al.}}}{{Tokumasu, Meurisse, Fillot, Vergne \emph {et~al.}}}} |
| 113 |
\bibcite{Ren06}{{27}{2006}{{Golubkov\ and\ Ren}}{{}}} |
| 114 |
\bibcite{Essex10}{{28}{2010}{{Orsi, Michel,\ and\ Essex}}{{}}} |
| 115 |
\bibcite{Essex11}{{29}{2011}{{Orsi\ and\ Essex}}{{}}} |
| 116 |
\bibcite{Ichiye10_1}{{30}{2010}{{Te, Tan,\ and\ Ichiye}}{{}}} |
| 117 |
\bibcite{Ichiye10_2}{{31}{2010{}}{{Te\ and\ Ichiye}}{{}}} |
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\bibcite{Ichiye10_3}{{32}{2010{}}{{Te\ and\ Ichiye}}{{}}} |
| 119 |
\bibcite{Gordon10}{{33}{2010}{{Ponder\ \emph {et~al.}}}{{Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio, Head-Gordon, Clark, Johnson,\ and\ Head-Gordon}}} |
| 120 |
\bibcite{Gordon07}{{34}{2007}{{Schnieders\ \emph {et~al.}}}{{Schnieders, Baker, Ren,\ and\ Ponder}}} |
| 121 |
\bibcite{Smith80}{{35}{1980}{{{de Leeuw}, Perram,\ and\ Smith}}{{}}} |
| 122 |
\bibcite{Lacman65}{{36}{1965}{{Lacman}}{{}}} |
| 123 |
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| 124 |
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| 125 |
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