--- trunk/electrostaticMethodsPaper/electrostaticMethods.tex	2006/03/06 23:20:15	2602
+++ trunk/electrostaticMethodsPaper/electrostaticMethods.tex	2006/03/07 20:46:45	2604
@@ -47,6 +47,10 @@ Notre Dame, Indiana 46556}
 
 \section{Introduction}
 
+In molecular simulations, proper accumulation of the electrostatic interactions is considered one of the most essential and computationally demanding tasks.  The strength and slow decay of the electrostatics are what give rise to their problematic importance.
+
+blah blah blah Ewald Sum Important blah blah blah
+
 In a recent paper by Wolf \textit{et al.}, a procedure was outlined for accumulation of electrostatic interactions in a simple pairwise fashion.\cite{Wolf99}  They took the observation that the electrostatic interaction is short-ranged in systems of charges and that charge neutralization within the cutoff spheres is crucial for potential stability, and they devised a pairwise summation method that ensures charge neutrality and gives results similar to those obtained using the Ewald summation.  The resulting shifted Coulomb potential (Eq. \ref{eq:WolfPot}) includes image-charges subtracted out through placement on the cutoff sphere and a distance-dependent damping function (identical to that seen in the real-space portion of the Ewald sum) to hasten energetic convergence
 \begin{equation}
 V(r_{ij})= \frac{q_iq_j \textrm{erfc}(\alpha r_{ij})}{r_{ij}}-\lim_{r_{ij}\rightarrow R_\textrm{c}}\left\{\frac{q_iq_j \textrm{erfc}(\alpha r_{ij})}{r_{ij}}\right\}.
@@ -81,9 +85,9 @@ Equation \ref{eq:SFPot} is similar to equation \ref{eq
 \end{equation}
 Equation \ref{eq:SFPot} is similar to equation \ref{eq:ZahnPot} derived by Zahn \textit{et al.}; however, there are two important differences.\cite{Zahn02} First, the $v_\textrm{c}$ term is simply equation \ref{eq:dampCoulomb} with $R_\textrm{c}$ supplied for $r_{ij}$.  This term is not present in equation \ref{eq:ZahnPot}, resulting in a discontinuity in the potential as particles cross $R_\textrm{c}$.  Second, the sign of the derivative portion is different.  The constant $v_\textrm{c}$ term is not going to have a presence in the forces after performing the derivative, but the negative sign does effect the derivative.  In fact, it introduces a discontinuity in the forces at the cutoff, because the force function is shifted in the wrong direction and doesn't cross zero at $R_\textrm{c}$.  Thus, these alterations make for an electrostatic summation method that is continuous in both the potential and forces and incorporates the pairwise sum considerations stressed by Wolf \textit{et al.}\cite{Wolf99}
 
-It is important to note that shifted force techniques have a drawback in that they alter the shape of the original potential.  We thereby lose a degree of clarity about the original formulation of the potential in order to gain functionality in dynamics simulations.  An alternative direction would be use the derivatives of the original potential for the forces.  This was addressed by Wolf \textit{et al.} as undesirable, because the effect of the image charges is neglected in the forces when they would expect there to be some pressure exerted due to their presence.\cite{Wolf99}  As a consequence the forces, though mathematically valid, may not be physically correct due to this missing component.  In Monte Carlo simulations, this argument is mute, because forces are not evaluated.  With this in mind, we decided to consider both the Shifted-Force technique described above and this Shifted-Potential technique to determine their usability in the evaluation of both energetic and dynamic results in simulations with electrostatics.
+It is important to note that shifted force techniques have a drawback in that they alter the shape of the original potential.  We thereby lose a degree of clarity about the original formulation of the potential in order to gain functionality in dynamics simulations.  An alternative direction would be use the derivatives of the original potential for the forces.  This was addressed by Wolf \textit{et al.} as undesirable, because the effect of the image charges is neglected in the forces when they would expect there to be some pressure exerted due to their presence.\cite{Wolf99}  As a consequence the forces, though mathematically valid, may not be physically correct due to this missing component.  In Monte Carlo simulations, this argument is mute, because forces are not evaluated.  We decided to consider both the Shifted-Force technique described above and this Shifted-Potential technique to determine their usability in the evaluation of both energetic and dynamic results in simulations with electrostatics.
 
-To this end, a variety of simulation situations were analyzed to determine the relative effectiveness of the adapted Wolf spherical truncation schemes at reproducing the results obtained using a smooth particle mesh Ewald (SPME) summation technique.\cite{Essmann95}  In addition to the Shifted-Potential and Shifted-Force adapted Wolf methods, both reaction field and uncorrected cutoff methods were included for comparison purposes.  The general usability of these methods in both Monte Carlo and Molecular Dynamics calculations was assessed through statistical analysis over the combined results from all of the following studied systems:
+A variety of simulation situations were assembled and analyzed to determine the relative effectiveness of the adapted Wolf spherical truncation schemes at reproducing the results obtained using a smooth particle mesh Ewald (SPME) summation technique.\cite{Essmann95}  In addition to the Shifted-Potential and Shifted-Force adapted Wolf methods, both reaction field and uncorrected cutoff methods were included for comparison purposes.  The general usability of these methods in both Monte Carlo and Molecular Dynamics calculations was assessed through statistical analysis over the combined results from all of the following studied systems:
 \begin{enumerate}
 \item Liquid Water
 \item Crystalline Water (Ice I$_\textrm{c}$)
@@ -93,7 +97,7 @@ To this end, a variety of simulation situations were a
 \item High Ionic Strength Solution of NaCl in Water 
 \item 6 \AA\  Radius Sphere of Argon in Water 
 \end{enumerate}
-Additional discussion on the results from the individual systems was also performed to identify limitations of the considered methods in specific systems.
+By studying these methods in systems composed entirely of neutral groups, charged particles, and mixtures of the two, we can either comment on possible system dependence or universal applicability of the techniques.
 
 \section{Methods}
 
@@ -108,7 +112,7 @@ Generation of the system configurations was dependent 
 \label{fig:argonSlice}
 \end{figure}
 
-All of these comparisons were performed with three different cutoff radii (9, 12, and 15 \AA) to investigate the cutoff radius dependence of the various techniques.  It should be noted that the damping parameter chosen in SPME, or so called ``Ewald Coefficient", has a significant effect on the energies and forces calculated.  Typical molecular mechanics packages default this to a value dependent on the cutoff radius and a tolerance (typically less than $1 \times 10^{-4}$ kcal/mol).  Smaller tolerances are typically associated with increased accuracy.\cite{Essmann95}  The default TINKER tolerance of $1 \times 10^{-8}$ was used in all SPME calculations, resulting in Ewald Coefficients of 0.4200, 0.3119, and 0.2476 \AA$^{-1}$ for cutoff radii of 9, 12, and 15 \AA\ respectively.
+All of these comparisons were performed with three different cutoff radii (9, 12, and 15 \AA) to investigate the cutoff radius dependence of the various techniques.  It should be noted that the damping parameter chosen in SPME, or so called ``Ewald Coefficient", has a significant effect on the energies and forces calculated.  Typical molecular mechanics packages default this to a value dependent on the cutoff radius and a tolerance (typically less than $1 \times 10^{-4}$ kcal/mol).  Smaller tolerances are typically associated with increased accuracy.\cite{Essmann95}  The default TINKER tolerance of $1 \times 10^{-8}$ kcal/mol was used in all SPME calculations, resulting in Ewald Coefficients of 0.4200, 0.3119, and 0.2476 \AA$^{-1}$ for cutoff radii of 9, 12, and 15 \AA\ respectively.
 
 \section{Results and Discussion}
 
@@ -253,6 +257,8 @@ where $S(r)$ is a switching function that smoothly zer
 
 \section{Conclusions}
 
+This investigation of pairwise electrostatic summation techniques shows that there are viable and more computationally efficient electrostatic summation techniques than the Ewald summation, chiefly methods derived from the damped Coulombic sum originally proposed by Wolf \textit{et al.}\cite{Wolf99,Zahn02}  In particular, the Shifted-Force method reformulated above
+
 \section{Acknowledgments}
 
 \newpage 
