--- trunk/electrostaticMethodsPaper/electrostaticMethods.tex 2006/04/26 14:20:17 2740 +++ trunk/electrostaticMethodsPaper/electrostaticMethods.tex 2006/04/26 17:41:25 2742 @@ -1,7 +1,7 @@ %\documentclass[prb,aps,twocolumn,tabularx]{revtex4} %\documentclass[aps,prb,preprint]{revtex4} -\documentclass[10pt]{article} -%\usepackage{endfloat} +\documentclass[11pt]{article} +\usepackage{endfloat} \usepackage{amsmath,bm} \usepackage{amssymb} \usepackage{epsf} @@ -20,14 +20,21 @@ \topmargin -21pt \headsep 10pt \textheight 9.0in \textwidth 6.5in \brokenpenalty=10000 -\renewcommand{\baselinestretch}{1.2} +%\renewcommand{\baselinestretch}{1.2} +\renewcommand{\baselinestretch}{2} \renewcommand\citemid{\ } % no comma in optional reference note +\AtBeginDelayedFloats{\renewcommand{\baselinestretch}{2}} %doublespace captions +\let\Caption\caption +\renewcommand\caption[1]{% + \Caption[#1]{}% +} + \begin{document} \title{Is the Ewald summation still necessary? \\ -Pairwise alternatives to the accepted standard for \\ -long-range electrostatics} +Pairwise alternatives to the accepted standard for +long-range electrostatics in molecular simulations} \author{Christopher J. Fennell and J. Daniel Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\ @@ -531,7 +538,7 @@ Fig. \ref{fig:linearFit}. \begin{figure} \centering -\includegraphics[width = 3.25in]{./dualLinear.pdf} +\includegraphics[width = \linewidth]{./dualLinear.pdf} \caption{Example least squares regressions of the configuration energy differences for SPC/E water systems. The upper plot shows a data set with a poor correlation coefficient ($R^2$), while the lower plot @@ -546,9 +553,9 @@ Results and discussion for the individual analysis of differences. Results and discussion for the individual analysis of each of the -system types appear in the supporting information, while the -cumulative results over all the investigated systems appears below in -section \ref{sec:EnergyResults}. +system types appear in the supporting information,\cite{EPAPSdeposit} +while the cumulative results over all the investigated systems appears +below in section \ref{sec:EnergyResults}. \subsection{Molecular Dynamics and the Force and Torque Vectors}\label{sec:MDMethods} We evaluated the pairwise methods (outlined in section @@ -717,7 +724,7 @@ figure \ref{fig:delE}. \begin{figure} \centering -\includegraphics[width=3.25in]{./delEplot.pdf} +\includegraphics[width=5.5in]{./delEplot.pdf} \caption{Statistical analysis of the quality of configurational energy differences for a given electrostatic method compared with the reference Ewald sum. Results with a value equal to 1 (dashed line) @@ -744,7 +751,7 @@ readers can consult the accompanying supporting inform significant improvement using the group-switched cutoff because the salt and salt solution systems contain non-neutral groups. Interested readers can consult the accompanying supporting information for a -comparison where all groups are neutral. +comparison where all groups are neutral.\cite{EPAPSdeposit} For the {\sc sp} method, inclusion of electrostatic damping improves the agreement with Ewald, and using an $\alpha$ of 0.2 \AA $^{-1}$ @@ -777,7 +784,7 @@ accumulation of the statistics from all of the system \begin{figure} \centering -\includegraphics[width=3.25in]{./frcMagplot.pdf} +\includegraphics[width=5.5in]{./frcMagplot.pdf} \caption{Statistical analysis of the quality of the force vector magnitudes for a given electrostatic method compared with the reference Ewald sum. Results with a value equal to 1 (dashed line) @@ -816,7 +823,7 @@ performs more favorably. \begin{figure} \centering -\includegraphics[width=3.25in]{./trqMagplot.pdf} +\includegraphics[width=5.5in]{./trqMagplot.pdf} \caption{Statistical analysis of the quality of the torque vector magnitudes for a given electrostatic method compared with the reference Ewald sum. Results with a value equal to 1 (dashed line) @@ -856,7 +863,7 @@ distributions of the combined set over all system type \begin{figure} \centering -\includegraphics[width=3.25in]{./frcTrqAngplot.pdf} +\includegraphics[width=5.5in]{./frcTrqAngplot.pdf} \caption{Statistical analysis of the width of the angular distribution that the force and torque vectors from a given electrostatic method make with their counterparts obtained using the reference Ewald sum. @@ -892,7 +899,7 @@ charged bodies, and this observation is investigated f particles in all seven systems, while torque vectors are only available for neutral molecular groups. Damping is more beneficial to charged bodies, and this observation is investigated further in the -accompanying supporting information. +accompanying supporting information.\cite{EPAPSdeposit} Although not discussed previously, group based cutoffs can be applied to both the {\sc sp} and {\sc sf} methods. The group-based cutoffs @@ -991,7 +998,7 @@ low-frequency portion of the power spectrum. \begin{figure} \centering -\includegraphics[width = 3.25in]{./vCorrPlot.pdf} +\includegraphics[width = \linewidth]{./vCorrPlot.pdf} \caption{Velocity autocorrelation functions of NaCl crystals at 1000 K using {\sc spme}, {\sc sf} ($\alpha$ = 0.0, 0.1, \& 0.2), and {\sc sp} ($\alpha$ = 0.2). The inset is a magnification of the area around @@ -1031,7 +1038,7 @@ noticeable effect on peak location or magnitude. \begin{figure} \centering -\includegraphics[width = 3.25in]{./spectraSquare.pdf} +\includegraphics[width = \linewidth]{./spectraSquare.pdf} \caption{Power spectra obtained from the velocity auto-correlation functions of NaCl crystals at 1000 K while using {\sc spme}, {\sc sf} ($\alpha$ = 0, 0.1, \& 0.2), and {\sc sp} ($\alpha$ = 0.2). The inset @@ -1070,7 +1077,7 @@ cutoff distance. \begin{figure} \centering -\includegraphics[width = 3.25in]{./increasedDamping.pdf} +\includegraphics[width = \linewidth]{./increasedDamping.pdf} \caption{Effect of damping on the two lowest-frequency phonon modes in the NaCl crystal at 1000~K. The undamped shifted force ({\sc sf}) method is off by less than 10 cm$^{-1}$, and increasing the