--- trunk/electrostaticMethodsPaper/electrostaticMethods.tex 2006/03/20 02:00:26 2639 +++ trunk/electrostaticMethodsPaper/electrostaticMethods.tex 2006/03/20 13:31:52 2640 @@ -87,7 +87,7 @@ Ewald summations, interaction shifting or classified as implicit methods (i.e., continuum dielectrics, static dipolar fields),\cite{Born20,Grossfield00} explicit methods (i.e., Ewald summations, interaction shifting or -trucation),\cite{Ewald21,Steinbach94} or a mixture of the two (i.e., +truncation),\cite{Ewald21,Steinbach94} or a mixture of the two (i.e., reaction field type methods, fast multipole methods).\cite{Onsager36,Rokhlin85} The explicit or mixed methods are often preferred because they incorporate dynamic solvent molecules in @@ -106,7 +106,7 @@ a variety of model systems and comparison methodologie modification to the direct pairwise sum, and they lack the added periodicity of the Ewald sum. Below, these methods are evaluated using a variety of model systems and comparison methodologies to establish -their useability in molecular simulations. +their usability in molecular simulations. \subsection{The Ewald Sum} The complete accumulation electrostatic interactions in a system with @@ -126,7 +126,7 @@ case of monopole electrostatics, eq. (\ref{eq:PBCSum}) $j$, and $\phi$ is Poisson's equation ($\phi(\mathbf{r}_{ij}) = q_i q_j |\mathbf{r}_{ij}|^{-1}$ for charge-charge interactions). In the case of monopole electrostatics, eq. (\ref{eq:PBCSum}) is -conditionally convergent and is discontiuous for non-neutral systems. +conditionally convergent and is discontinuous for non-neutral systems. This electrostatic summation problem was originally studied by Ewald for the case of an infinite crystal.\cite{Ewald21}. The approach he @@ -176,7 +176,7 @@ real-space or reciprocal space portion of the summatio direct and reciprocal-space portions of the summation. The choice of the magnitude of this value allows one to select whether the real-space or reciprocal space portion of the summation is an -$\mathscr{O}(N^2)$ calcualtion (with the other being +$\mathscr{O}(N^2)$ calculation (with the other being $\mathscr{O}(N)$).\cite{Sagui99} With appropriate choice of $\alpha$ and thoughtful algorithm development, this cost can be brought down to $\mathscr{O}(N^{3/2})$.\cite{Perram88} The typical route taken to @@ -212,7 +212,7 @@ considering the use of the Ewald summation where the i artificially stabilized by the periodic replicas introduced by the Ewald summation.\cite{Weber00} Thus, care ought to be taken when considering the use of the Ewald summation where the intrinsic -perodicity may negatively affect the system dynamics. +periodicity may negatively affect the system dynamics. \subsection{The Wolf and Zahn Methods} @@ -230,7 +230,7 @@ the real-space portion of the Ewald sum) to aid conver and a distance-dependent damping function (identical to that seen in the real-space portion of the Ewald sum) to aid convergence \begin{equation} -V_{\textrm{Wolf}}(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\}. +V_{\textrm{Wolf}}(r_{ij})= \frac{q_i q_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\}. \label{eq:WolfPot} \end{equation} Eq. (\ref{eq:WolfPot}) is essentially the common form of a shifted @@ -738,7 +738,7 @@ al.},\cite{Wolf99} and this correction indeed improves Correcting the resulting charged cutoff sphere is one of the purposes of the damped Coulomb summation proposed by Wolf \textit{et al.},\cite{Wolf99} and this correction indeed improves the results as -seen in the Shifted-Potental rows. While the undamped case of this +seen in the {\sc sp} rows. While the undamped case of this method is a significant improvement over the pure cutoff, it still doesn't correlate that well with SPME. Inclusion of potential damping improves the results, and using an $\alpha$ of 0.2 \AA $^{-1}$ shows @@ -951,7 +951,7 @@ the point charges for the pairwise summation methods; increased, these peaks are smoothed out, and approach the SPME curve. The damping acts as a distance dependent Gaussian screening of the point charges for the pairwise summation methods; thus, the -collisions are more elastic in the undamped {\sc sf} potental, and the +collisions are more elastic in the undamped {\sc sf} potential, and the stiffness of the potential is diminished as the electrostatic interactions are softened by the damping function. With $\alpha$ values of 0.2 \AA$^{-1}$, the {\sc sf} and {\sc sp} functions are