| 3 |
|
\usepackage{endfloat} |
| 4 |
|
\usepackage{amsmath} |
| 5 |
|
\usepackage{amssymb} |
| 6 |
– |
%\usepackage{ifsym} |
| 6 |
|
\usepackage{epsf} |
| 7 |
|
\usepackage{times} |
| 8 |
|
\usepackage{mathptm} |
| 10 |
|
\usepackage{tabularx} |
| 11 |
|
\usepackage{graphicx} |
| 12 |
|
\usepackage{booktabs} |
| 13 |
+ |
\usepackage{bibentry} |
| 14 |
+ |
\usepackage{mathrsfs} |
| 15 |
|
%\usepackage{berkeley} |
| 16 |
|
\usepackage[ref]{overcite} |
| 17 |
|
\pagestyle{plain} |
| 25 |
|
|
| 26 |
|
\begin{document} |
| 27 |
|
|
| 28 |
< |
\title{Is the Ewald Summation necessary in typical molecular simulations: Alternatives to the accepted standard of cutoff policies} |
| 28 |
> |
\title{Is the Ewald Summation necessary? : Pairwise alternatives to the accepted standard for long-range electrostatics} |
| 29 |
|
|
| 30 |
|
\author{Christopher J. Fennell and J. Daniel Gezelter \\ |
| 31 |
|
Department of Chemistry and Biochemistry\\ |
| 36 |
|
|
| 37 |
|
\maketitle |
| 38 |
|
%\doublespacing |
| 39 |
< |
|
| 39 |
> |
\nobibliography{} |
| 40 |
|
\begin{abstract} |
| 41 |
+ |
A new method for accumulating electrostatic interactions was derived from the previous efforts described in \bibentry{Wolf99} and \bibentry{Zahn02} as a possible replacement for lattice sum methods in molecular simulations. Comparisons were performed with this and other pairwise electrostatic summation techniques against the smooth particle mesh Ewald (SPME) summation to see how well they reproduce the energetics and dynamics of a variety of simulation types. The newly derived Shifted-Force technique shows a remarkable ability to reproduce the behavior exhibited in simulations using SPME with an $\mathscr{O}(N)$ computational cost, equivalent to merely the real-space portion of the lattice summation. |
| 42 |
|
\end{abstract} |
| 43 |
|
|
| 44 |
|
%\narrowtext |
| 45 |
|
|
| 46 |
< |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| 46 |
> |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| 47 |
|
% BODY OF TEXT |
| 48 |
< |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| 48 |
> |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| 49 |
|
|
| 50 |
|
\section{Introduction} |
| 51 |
|
|
| 52 |
< |
In this paper, 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. 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: |
| 52 |
> |
In molecular simulations, proper accumulation of the electrostatic interactions is considered one of the most essential and computationally demanding tasks. |
| 53 |
> |
|
| 54 |
> |
\subsection{The Ewald Sum} |
| 55 |
> |
blah blah blah Ewald Sum Important blah blah blah |
| 56 |
> |
|
| 57 |
> |
\begin{figure} |
| 58 |
> |
\centering |
| 59 |
> |
\includegraphics[width = 3.25in]{./ewaldProgression.pdf} |
| 60 |
> |
\caption{How the application of the Ewald summation has changed with the increase in computer power. Initially, only small numbers of particles could be studied, and the Ewald sum acted to replicate the unit cell charge distribution out to convergence. Now, much larger systems of charges are investigated with fixed distance cutoffs. The calculated structure factor is used to sum out to great distance, and a surrounding dielectric term is included.} |
| 61 |
> |
\label{fig:ewaldTime} |
| 62 |
> |
\end{figure} |
| 63 |
> |
|
| 64 |
> |
\subsection{The Wolf and Zahn Methods} |
| 65 |
> |
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 effective electrostatic interaction is short-ranged in systems of charges and that charge neutralization within the cutoff spheres is crucial for potential stability. 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 aid energetic convergence |
| 66 |
> |
\begin{equation} |
| 67 |
> |
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\}. |
| 68 |
> |
\label{eq:WolfPot} |
| 69 |
> |
\end{equation} |
| 70 |
> |
In order to use this potential in molecular dynamics simulations, Wolf \textit{et al.} suggested taking the derivative of this potential, followed by evaluation of the limit to give the following forces, |
| 71 |
> |
\begin{equation} |
| 72 |
> |
F^{\textrm{Wolf}}(r_{ij}) = q_iq_j\left\{\left[-\frac{\textrm{erfc}(\alpha r_{ij})}{r^2_{ij}}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp{(-\alpha^2r_{ij}^2)}}{r_{ij}}\right]+\left[\frac{\textrm{erfc}\left(\alpha R_{\textrm{c}}\right)}{R_{\textrm{c}}^2}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp{\left(-\alpha^2R_{\textrm{c}}^2\right)}}{R_{\textrm{c}}}\right]\right\}. |
| 73 |
> |
\label{eq:WolfForces} |
| 74 |
> |
\end{equation} |
| 75 |
> |
More recently, Zahn \textit{et al.} investigated this electrostatic summation method for use in simulations involving water.\cite{Zahn02} In their work, they point out that the method as proposed is problematic for use in Molecular Dynamics simulations, because the forces and derivative of the potential are not equivalent. This comes about from the procedure of taking the limit shown in equation \ref{eq:WolfPot} after calculating the derivatives.\cite{Wolf99} Zahn \textit{et al.} proposed a shifted force adaptation of this ``Wolf summation method" as a way to use this technique in Molecular Dynamics simulations. Taking the integral of the forces shown in equation \ref{eq:WolfForces}, they obtained a new shifted damped Coulomb potential |
| 76 |
> |
\begin{equation} |
| 77 |
> |
V^{\textrm{Zahn}}(r_{ij}) = q_iq_j\left\{\frac{\mathrm{erfc}\left(\alpha r_{ij}\right)}{r_{ij}}-\left[\frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}^2}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp\left(-\alpha^2R_\mathrm{c}^2\right)}{R_\mathrm{c}}\right]\left(r_{ij}-R_\mathrm{c}\right)\right\}. |
| 78 |
> |
\label{eq:ZahnPot} |
| 79 |
> |
\end{equation} |
| 80 |
> |
They showed that this new potential does well in capturing the structural and dynamic properties present when using the Ewald sum with the models of water used in their simulations. |
| 81 |
> |
|
| 82 |
> |
\subsection{Simple Forms for Pairwise Electrostatics} |
| 83 |
> |
The potentials proposed by Wolf \textit{et al.} and Zahn \textit{et al.} are constructed using two different (and separable) computational tricks: shifting through use of image charges and damping of the electrostatic interaction. Wolf \textit{et al.} treated the development of their summation method as a progressive application of these techniques,\cite{Wolf99} while Zahn \textit{et al.} founded their shifted force adaptation \ref{eq:ZahnPot} on what they called "the formally incorrect prescription for the derivation of damped Coulomb pair forces".\cite{Zahn02} Below, we consider the ideas encompassing these electrostatic summation method formulations and clarify their development. |
| 84 |
> |
|
| 85 |
> |
Starting with the original observation that the effective range of the electrostatic interaction in condensed phases is considerably less than the $r^{-1}$ in vacuum, either the shifting or the distance-dependent damping technique could be used as a foundation for the summation method. Wolf \textit{et al.} made the additional observation that charge neutralization within the cutoff sphere plays a significant role in energy convergence; thus, shifting through the use of image charges was taken as the initial step. Using these image charges, the electrostatic summation is forced to converge at the cutoff radius. We can incorporate the methods of Wolf \textit{et al.} and Zahn \textit{et al.} by considering the standard shifted force potential |
| 86 |
> |
\begin{equation} |
| 87 |
> |
V^\textrm{SF}(r_{ij}) = \begin{cases} v(r_{ij})-v_\textrm{c}-\left[\frac{\textrm{d}v(r_{ij})}{\textrm{d}r_{ij}}\right]_{r_{ij}=R_\textrm{c}}(r_{ij}-R_\textrm{c}) &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 88 |
> |
\end{cases}, |
| 89 |
> |
\label{eq:shiftingForm} |
| 90 |
> |
\end{equation} |
| 91 |
> |
where $v(r_{ij})$ is the unshifted form of the potential, and $v_c$ is $v(R_\textrm{c})$ and insures the potential goes to zero at the cutoff radius.\cite{Allen87} If the derivative term is taken to be zero, we are left with the shifted Coulomb potential devised by Wolf \textit{et al.},\cite{Wolf99} |
| 92 |
> |
\begin{equation} |
| 93 |
> |
V^\textrm{WSP}(r_{ij}) = \begin{cases} q_iq_j\left(\frac{1}{r_{ij}}-\frac{1}{R_\textrm{c}}\right) &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 94 |
> |
\end{cases}. |
| 95 |
> |
\label{eq:WolfSP} |
| 96 |
> |
\end{equation} |
| 97 |
> |
The forces associated with this potential are obtained by taking the derivative, resulting in the following, |
| 98 |
> |
\begin{equation} |
| 99 |
> |
F^\textrm{WSP}(r_{ij}) = \begin{cases} q_iq_j\left(-\frac{1}{r_{ij}^2}\right) &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 100 |
> |
\end{cases}. |
| 101 |
> |
\label{eq:FWolfSP} |
| 102 |
> |
\end{equation} |
| 103 |
> |
These forces are identical to the forces of the standard electrostatic interaction, and this was addressed by Wolf \textit{et al.} as undesirable. They pointed out that 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. Additionally, there is a discontinuity in the forces. This can be remedied with the use of a switching function to zero the potential and forces smoothly as particles near $R_\textrm{c}$. |
| 104 |
> |
|
| 105 |
> |
If the derivative term in equation \ref{eq:shiftingForm} is evaluated, we obtain an hitherto undiscussed shifted force Coulomb potential, |
| 106 |
> |
\begin{equation} |
| 107 |
> |
V^\textrm{SF}(r_{ij}) = \begin{cases} q_iq_j\left\{\frac{1}{r_{ij}}-\frac{1}{R_\textrm{c}}+\left[\frac{1}{R_\textrm{c}^2}\right](r_{ij}-R_\textrm{c})\right\} &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 108 |
> |
\end{cases}. |
| 109 |
> |
\label{eq:SFPot} |
| 110 |
> |
\end{equation} |
| 111 |
> |
Taking the derivative of this shifted force potential gives the following forces, |
| 112 |
> |
\begin{equation} |
| 113 |
> |
F^\textrm{SF}(r_{ij}) = \begin{cases} q_iq_j\left(-\frac{1}{r_{ij}^2}+\frac{1}{R_\textrm{c}^2}\right) &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 114 |
> |
\end{cases}. |
| 115 |
> |
\label{eq:SFForces} |
| 116 |
> |
\end{equation} |
| 117 |
> |
Using this formulation rather than the simple shifted potential (Eq. \ref{eq:WolfSP}) means that there are no discontinuities in the forces in addition to the potential. This form also has the benefit that the image charges have a force presence, addressing the concerns about a missing physical component. One side effect of this treatment is a slight alteration in the shape of the potential that comes about from the derivative term. Thus, a degree of clarity about the original formulation of the potential is lost in order to gain functionality in dynamics simulations. |
| 118 |
> |
|
| 119 |
> |
Wolf \textit{et al.} originally discussed the energetics of the shifted Coulomb potential (Eq. \ref{eq:WolfSP}), and they found that it was still insufficient for accurate determination of the energy. The energy would fluctuate around the expected value with increasing cutoff radius, but the oscillations appeared to be converging toward the correct value.\cite{Wolf99} A damping function was incorporated to accelerate convergence; and though alternative functional forms could be used,\cite{Jones56,Heyes81} the complimentary error function was chosen to draw parallels to the Ewald summation. Incorporating damping into the simple Coulomb potential, |
| 120 |
> |
\begin{equation} |
| 121 |
> |
v(r_{ij}) = \frac{\mathrm{erfc}\left(\alpha r_{ij}\right)}{r_{ij}}, |
| 122 |
> |
\label{eq:dampCoulomb} |
| 123 |
> |
\end{equation} |
| 124 |
> |
the shifted potential (Eq. \ref{eq:WolfSP}) can be rederived \textit{via} equation \ref{eq:shiftingForm}, |
| 125 |
> |
\begin{equation} |
| 126 |
> |
V^{\textrm{DSP}}(r_{ij}) = \begin{cases} q_iq_j\left[\frac{\textrm{erfc}(\alpha r_{ij})}{r_{ij}}-\frac{\textrm{erfc}(\alpha R_\textrm{c})}{R_\textrm{c}}\right] &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 127 |
> |
\end{cases}. |
| 128 |
> |
\label{eq:DSPPot} |
| 129 |
> |
\end{equation} |
| 130 |
> |
The derivative of this Shifted-Potential can be taken to obtain forces for use in MD, |
| 131 |
> |
\begin{equation} |
| 132 |
> |
F^{\textrm{DSP}}(r_{ij}) = \begin{cases} q_iq_j\left[\frac{\textrm{erfc}(\alpha r_{ij})}{r^2_{ij}}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp{(-\alpha^2r_{ij}^2)}}{r_{ij}}\right] &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 133 |
> |
\end{cases}. |
| 134 |
> |
\label{eq:DSPForces} |
| 135 |
> |
\end{equation} |
| 136 |
> |
Again, this Shifted-Potential suffers from a discontinuity in the forces, and a lack of an image-charge component in the forces. To remedy these concerns, a Shifted-Force variant is obtained by inclusion of the derivative term in equation \ref{eq:shiftingForm} to give, |
| 137 |
> |
\begin{equation} |
| 138 |
> |
V^\mathrm{DSF}(r_{ij}) = \begin{cases} q_iq_j\left\{\frac{\mathrm{erfc}\left(\alpha r_{ij}\right)}{r_{ij}}-\frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}}\left[\frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}^2}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp\left(-\alpha^2R_\mathrm{c}^2\right)}{R_\mathrm{c}}\right]\left(r_{ij}-R_\mathrm{c}\right)\right\} &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 139 |
> |
\end{cases}. |
| 140 |
> |
\label{eq:DSFPot} |
| 141 |
> |
\end{equation} |
| 142 |
> |
The derivative of the above potential gives the following forces, |
| 143 |
> |
\begin{equation} |
| 144 |
> |
F^\mathrm{DSF}(r_{ij}) = \begin{cases} q_iq_j\left\{-\left[\frac{\textrm{erfc}(\alpha r_{ij})}{r^2_{ij}}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp{(-\alpha^2r_{ij}^2)}}{r_{ij}}\right]+\left[\frac{\textrm{erfc}(\alpha R_{\textrm{c}})}{R_{\textrm{c}}^2}+\frac{2\alpha}{\pi^{1/2}}\frac{\exp{(-\alpha^2R_{\textrm{c}}^2)}}{R_{\textrm{c}}}\right]\right\} &\quad r_{ij}\leqslant R_\textrm{c} \\ 0 &\quad r_{ij}>R_\textrm{c} |
| 145 |
> |
\end{cases}. |
| 146 |
> |
\label{eq:DSFForces} |
| 147 |
> |
\end{equation} |
| 148 |
> |
|
| 149 |
> |
This new Shifted-Force potential 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 from equation \ref{eq:shiftingForm} is equal to equation \ref{eq:dampCoulomb} with $R_\textrm{c}$ supplied for $r_{ij}$. This term is not present in the Zahn potential, resulting in a discontinuity 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} |
| 150 |
> |
|
| 151 |
> |
\section{Methods} |
| 152 |
> |
|
| 153 |
> |
\subsection{What Qualities are Important?}\label{sec:Qualities} |
| 154 |
> |
In classical molecular mechanics simulations, there are two primary techniques utilized to obtain information about the system of interest: Monte Carlo (MC) and Molecular Dynamics (MD). Both of these techniques utilize pairwise summations of interactions between particle sites, but they use these summations in different ways. |
| 155 |
> |
|
| 156 |
> |
In MC, the potential energy difference between two subsequent configurations dictates the progression of MC sampling. Going back to the origins of this method, the Canonical ensemble acceptance criteria laid out by Metropolis \textit{et al.} states that a subsequent configuration is accepted if $\Delta E < 0$ or if $\xi < \exp(-\Delta E/kT)$, where $\xi$ is a random number between 0 and 1.\cite{Metropolis53} Maintaining a consistent $\Delta E$ when using an alternate method for handling the long-range electrostatics ensures proper sampling within the ensemble. |
| 157 |
> |
|
| 158 |
> |
In MD, the derivative of the potential directs how the system will progress in time. Consequently, the force and torque vectors on each body in the system dictate how it develops as a whole. If the magnitude and direction of these vectors are similar when using alternate electrostatic summation techniques, the dynamics in the near term will be indistinguishable. Because error in MD calculations is cumulative, one should expect greater deviation in the long term trajectories with greater differences in these vectors between configurations using different long-range electrostatics. |
| 159 |
> |
|
| 160 |
> |
\subsection{Monte Carlo and the Energy Gap}\label{sec:MCMethods} |
| 161 |
> |
Evaluation of the pairwise summation techniques (outlined in section \ref{sec:ESMethods}) for use in MC simulations was performed through study of the energy differences between conformations. Considering the SPME results to be the correct or desired behavior, ideal performance of a tested method was taken to be agreement between the energy differences calculated. Linear least squares regression of the $\Delta E$ values between configurations using SPME against $\Delta E$ values using tested methods provides a quantitative comparison of this agreement. Unitary results for both the correlation and correlation coefficient for these regressions indicate equivalent energetic results between the methods. The correlation is the slope of the plotted data while the correlation coefficient ($R^2$) is a measure of the of the data scatter around the fitted line and tells about the quality of the fit (Fig. \ref{fig:linearFit}). |
| 162 |
> |
|
| 163 |
> |
\begin{figure} |
| 164 |
> |
\centering |
| 165 |
> |
\includegraphics[width=3.25in]{./linearFit.pdf} |
| 166 |
> |
\caption{Example least squares regression of the $\Delta E$ between configurations for the SF method against SPME in the pure water system. } |
| 167 |
> |
\label{fig:linearFit} |
| 168 |
> |
\end{figure} |
| 169 |
> |
|
| 170 |
> |
Each system type (detailed in section \ref{sec:RepSims}) studied consisted of 500 independent configurations, each equilibrated from higher temperature trajectories. Thus, 124,750 $\Delta E$ data points are used in a regression of a single system type. 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}. |
| 171 |
> |
|
| 172 |
> |
\subsection{Molecular Dynamics and the Force and Torque Vectors}\label{sec:MDMethods} |
| 173 |
> |
Evaluation of the pairwise methods (outlined in section \ref{sec:ESMethods}) for use in MD simulations was performed through comparison of the force and torque vectors obtained with those from SPME. Both the magnitude and the direction of these vectors on each of the bodies in the system were analyzed. For the magnitude of these vectors, linear least squares regression analysis can be performed as described previously for comparing $\Delta E$ values. Instead of a single value between two system configurations, there is a value for each particle in each configuration. For a system of 1000 water molecules and 40 ions, there are 1040 force vectors and 1000 torque vectors. With 500 configurations, this results in 520,000 force and 500,000 torque vector comparisons samples for each system type. |
| 174 |
> |
|
| 175 |
> |
The force and torque vector directions were investigated through measurement of the angle ($\theta$) formed between those from the particular method and those from SPME |
| 176 |
> |
\begin{equation} |
| 177 |
> |
\theta_F = \frac{\vec{F}_\textrm{SPME}}{|\vec{F}_\textrm{SPME}|}\cdot\frac{\vec{F}_\textrm{Method}}{|\vec{F}_\textrm{Method}|}. |
| 178 |
> |
\end{equation} |
| 179 |
> |
Each of these $\theta$ values was accumulated in a distribution function, weighted by the area on the unit sphere. Non-linear fits were used to measure the shape of the resulting distributions. |
| 180 |
> |
|
| 181 |
> |
\begin{figure} |
| 182 |
> |
\centering |
| 183 |
> |
\includegraphics[width=3.25in]{./gaussFit.pdf} |
| 184 |
> |
\caption{Sample fit of the angular distribution of the force vectors over all of the studied systems. Gaussian fits were used to obtain values for the variance in force and torque vectors used in the following figure.} |
| 185 |
> |
\label{fig:gaussian} |
| 186 |
> |
\end{figure} |
| 187 |
> |
|
| 188 |
> |
Figure \ref{fig:gaussian} shows an example distribution with applied non-linear fits. The solid line is a Gaussian profile, while the dotted line is a Voigt profile, a convolution of a Gaussian and a Lorentzian. Since this distribution is a measure of angular error between two different electrostatic summation methods, there is particular reason for the profile to adhere to a specific shape. Because of this and the Gaussian profile's more statistically meaningful properties, Gaussian fits was used to compare all the tested methods. The variance ($\sigma^2$) was extracted from each of these fits and was used to compare distribution widths. Values of $\sigma^2$ near zero indicate vector directions indistinguishable from those calculated when using SPME. |
| 189 |
> |
|
| 190 |
> |
\subsection{Long-Time and Collective Motion}\label{sec:LongTimeMethods} |
| 191 |
> |
Evaluation of the long-time dynamics of charged systems was performed by considering the NaCl crystal system while using a subset of the best performing pairwise methods. The NaCl crystal was chosen to avoid possible complications involving the propagation techniques of orientational motion in molecular systems. To enhance the atomic motion, these crystals were equilibrated at 1000 K, near the experimental $T_m$ for NaCl. Simulations were performed under the microcanonical ensemble, and velocity autocorrelation functions (Eq. \ref{eq:vCorr}) were computed for each of the trajectories, |
| 192 |
> |
\begin{equation} |
| 193 |
> |
C_v(t) = \langle v_i(0)\cdot v_i(t)\rangle. |
| 194 |
> |
\label{eq:vCorr} |
| 195 |
> |
\end{equation} |
| 196 |
> |
Velocity autocorrelation functions require detailed short time data and long trajectories for good statistics, thus velocity information was saved every 5 fs over 100 ps trajectories. The power spectrum ($I(\omega)$) is obtained via Fourier transform of the autocorrelation function |
| 197 |
> |
\begin{equation} |
| 198 |
> |
I(\omega) = \frac{1}{2\pi}\int^{\infty}_{-\infty}C_v(t)e^{-i\omega t}dt, |
| 199 |
> |
\label{eq:powerSpec} |
| 200 |
> |
\end{equation} |
| 201 |
> |
where the frequency, $\omega=0,\ 1,\ ...,\ N-1$. |
| 202 |
> |
|
| 203 |
> |
\subsection{Representative Simulations}\label{sec:RepSims} |
| 204 |
> |
A variety of common and representative simulations were analyzed to determine the relative effectiveness of the pairwise summation techniques in reproducing the energetics and dynamics exhibited by SPME. The studied systems were as follows: |
| 205 |
|
\begin{enumerate} |
| 206 |
|
\item Liquid Water |
| 207 |
|
\item Crystalline Water (Ice I$_\textrm{c}$) |
| 211 |
|
\item High Ionic Strength Solution of NaCl in Water |
| 212 |
|
\item 6 \AA\ Radius Sphere of Argon in Water |
| 213 |
|
\end{enumerate} |
| 214 |
< |
Additional discussion on the results from the individual systems was also performed to identify limitations of the considered methods in specific systems. |
| 214 |
> |
By utilizing the pairwise techniques (outlined in section \ref{sec:ESMethods}) in systems composed entirely of neutral groups, charged particles, and mixtures of the two, we can comment on possible system dependence and/or universal applicability of the techniques. |
| 215 |
|
|
| 216 |
< |
\section{Methods} |
| 216 |
> |
Generation of the system configurations was dependent on the system type. For the solid and liquid water configurations, configuration snapshots were taken at regular intervals from higher temperature 1000 SPC/E water molecule trajectories and each equilibrated individually. The solid and liquid NaCl systems consisted of 500 Na+ and 500 Cl- ions and were selected and equilibrated in the same fashion as the water systems. For the low and high ionic strength NaCl solutions, 4 and 40 ions were first solvated in a 1000 water molecule boxes respectively. Ion and water positions were then randomly swapped, and the resulting configurations were again equilibrated individually. Finally, for the Argon/Water "charge void" systems, the identities of all the SPC/E waters within 6 \AA\ of the center of the equilibrated water configurations were converted to argon (Fig. \ref{fig:argonSlice}). |
| 217 |
|
|
| 64 |
– |
In each of the simulated systems, 500 distinct configurations were generated, and the electrostatic summation methods were compared via sequential application on each of these fixed configurations. The methods compared include SPME, the aforementioned Shifted Potential and Shifted Force methods - both with damping parameters ($\alpha$) of 0, 0.1, 0.2, and 0.3 \AA$^{-1}$, reaction field with an infinite dielectric constant, and an unmodified cutoff. Group-based cutoffs with a fifth-order polynomial switching function were necessary for the reaction field simulations and were utilized in the SP, SF, and pure cutoff methods for comparison to the standard lack of group-based cutoffs with a hard truncation. |
| 65 |
– |
|
| 66 |
– |
Generation of the system configurations was dependent on the system type. For the solid and liquid water configurations, configuration snapshots were taken at regular intervals from higher temperature 1000 SPC/E water molecule trajectories and each equilibrated individually. The solid and liquid NaCl systems consisted of 500 Na+ and 500 Cl- ions and were selected and equilibrated in the same fashion as the water systems. For the low and high ionic strength NaCl solutions, 4 and 40 ions were first solvated in a 1000 water molecule boxes respectively. Ion and water positions were then randomly swapped, and the resulting configurations were again equilibrated individually. Finally, for the Argon/Water "charge void" systems, the identities of all the SPC/E waters within 6 \AA\ of the center of the equilibrated water configurations were converted to argon (Fig. \ref{argonSlice}). |
| 67 |
– |
|
| 218 |
|
\begin{figure} |
| 219 |
|
\centering |
| 220 |
|
\includegraphics[width=3.25in]{./slice.pdf} |
| 221 |
|
\caption{A slice from the center of a water box used in a charge void simulation. The darkened region represents the boundary sphere within which the water molecules were converted to argon atoms.} |
| 222 |
< |
\label{argonSlice} |
| 222 |
> |
\label{fig:argonSlice} |
| 223 |
|
\end{figure} |
| 224 |
|
|
| 225 |
< |
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 $1 \times 10^{-5}$ kcal/mol). We chose a tolerance of $1 \times 10^{-8}$, resulting in Ewald Coefficients of 0.4200, 0.3119, and 0.2476 \AA$^{-1}$ for cutoff radii of 9, 12, and 15 \AA\ respectively. |
| 225 |
> |
\subsection{Electrostatic Summation Methods}\label{sec:ESMethods} |
| 226 |
> |
Electrostatic summation method comparisons were performed using SPME, the Shifted-Potential and Shifted-Force methods - both with damping parameters ($\alpha$) of 0.0, 0.1, 0.2, and 0.3 \AA$^{-1}$ (no, weak, moderate, and strong damping respectively), reaction field with an infinite dielectric constant, and an unmodified cutoff. Group-based cutoffs with a fifth-order polynomial switching function were necessary for the reaction field simulations and were utilized in the SP, SF, and pure cutoff methods for comparison to the standard lack of group-based cutoffs with a hard truncation. The SPME calculations were performed using the TINKER implementation of SPME,\cite{Ponder87} while all other method calculations were performed using the OOPSE molecular mechanics package.\cite{Meineke05} |
| 227 |
|
|
| 228 |
+ |
These methods were additionally evaluated with three different cutoff radii (9, 12, and 15 \AA) to investigate possible cutoff radius dependence. 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 in the real-space portion of the summation.\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. |
| 229 |
+ |
|
| 230 |
|
\section{Results and Discussion} |
| 231 |
|
|
| 232 |
< |
\subsection{$\Delta E$ Comparison} |
| 233 |
< |
In order to evaluate the performance of the adapted Wolf Shifted Potential and Shifted Force electrostatic summation methods for Monte Carlo simulations, the energy differences between configurations need to be compared to the results using SPME. Considering the SPME results to be the correct or desired behavior, ideal performance of a tested method is taken to be agreement between the energy differences calculated. Linear least squares regression of the $\Delta E$ values between configurations using SPME against $\Delta E$ values using tested methods provides a quantitative comparison of this agreement. Unitary results for both the correlation and correlation coefficient for these regressions indicate equivalent energetic results between the methods. The correlation is the slope of the plotted data while the correlation coefficient ($R^2$) is a measure of the of the data scatter around the fitted line and gives an idea of the quality of the fit (Fig. \ref{linearFit}). |
| 232 |
> |
\subsection{Configuration Energy Differences}\label{sec:EnergyResults} |
| 233 |
> |
In order to evaluate the performance of the pairwise electrostatic summation methods for Monte Carlo simulations, the energy differences between configurations were compared to the values obtained when using SPME. The results for the subsequent regression analysis are shown in figure \ref{fig:delE}. |
| 234 |
|
|
| 235 |
|
\begin{figure} |
| 236 |
|
\centering |
| 84 |
– |
\includegraphics[width=3.25in]{./linearFit.pdf} |
| 85 |
– |
\caption{Example least squares regression of the $\Delta E$ between configurations for the SF method against SPME in the pure water system. } |
| 86 |
– |
\label{linearFit} |
| 87 |
– |
\end{figure} |
| 88 |
– |
|
| 89 |
– |
With 500 independent configurations, 124,750 $\Delta E$ data points are used in a regression of a single system. Results and discussion for the individual analysis of each of the system types appear in the supporting information. To probe the applicability of each method in the general case, all the different system types were included in a single regression. The results for this regression are shown in figure \ref{delE}. |
| 90 |
– |
|
| 91 |
– |
\begin{figure} |
| 92 |
– |
\centering |
| 237 |
|
\includegraphics[width=3.25in]{./delEplot.pdf} |
| 238 |
< |
\caption{The results from the statistical analysis of the $\Delta$E results for all the system types at 9 \AA\ (${\bullet}$), 12 \AA\ ($\blacksquare$), and 15 \AA\ ($\blacktriangledown$) cutoff radii. Results close to a value of 1 (dashed line) indicate $\Delta E$ values from that particular method (listed on the left) are nearly indistinguishable from those obtained from SPME. Reaction Field results do not include NaCl crystal or melt configurations.} |
| 239 |
< |
\label{delE} |
| 238 |
> |
\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) indicate $\Delta E$ values indistinguishable from those obtained using SPME. Different values of the cutoff radius are indicated with different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = inverted triangles).} |
| 239 |
> |
\label{fig:delE} |
| 240 |
|
\end{figure} |
| 241 |
|
|
| 242 |
< |
In figure \ref{delE}, it is apparent that it is unreasonable to expect realistic results using an unmodified cutoff. This is not all that surprising since this results in large energy fluctuations as atoms move in and out of the cutoff radius. These fluctuations can be alleviated to some degree by using group based cutoffs with a switching function. The Group Switch Cutoff row doesn't show a significant improvement in this plot because the salt and salt solution systems contain non-neutral groups, see the accompanying supporting information for a comparison where all groups are neutral. Correcting the resulting charged cutoff sphere is one of the purposes of the shifted potential proposed by Wolf \textit{et al.}, and this correction indeed improves the results as seen in the Shifted Potental 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 an excellent correlation and quality of fit with the SPME results, particularly with a cutoff radius greater than 12 \AA . Use of a larger damping parameter is more helpful for the shortest cutoff shown, but it has a detrimental effect on simulations with larger cutoffs. This trend is repeated in the Shifted Force rows, where increasing damping results in progressively poorer correlation; however, damping looks to be unnecessary with this method. Overall, the undamped case is the best performing set, as the correlation and quality of fits are consistently superior regardless of the cutoff distance. This result is beneficial in that the undamped case is less computationally prohibitive do to the lack of complimentary error function calculation when performing the electrostatic pair interaction. The reaction field results illustrates some of that method's limitations, primarily that it was developed for use in homogenous systems; although it does provide results that are an improvement over those from an unmodified cutoff. |
| 242 |
> |
In this figure, it is apparent that it is unreasonable to expect realistic results using an unmodified cutoff. This is not all that surprising since this results in large energy fluctuations as atoms move in and out of the cutoff radius. These fluctuations can be alleviated to some degree by using group based cutoffs with a switching function.\cite{Steinbach94} The Group Switch Cutoff row doesn't show a significant improvement in this plot because the salt and salt solution systems contain non-neutral groups, see the accompanying supporting information for a comparison where all groups are neutral. |
| 243 |
|
|
| 244 |
< |
\subsection{Force Magnitude Comparison} |
| 244 |
> |
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 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 an excellent correlation and quality of fit with the SPME results, particularly with a cutoff radius greater than 12 \AA . Use of a larger damping parameter is more helpful for the shortest cutoff shown, but it has a detrimental effect on simulations with larger cutoffs. In the Shifted-Force sets, increasing damping results in progressively poorer correlation. Overall, the undamped case is the best performing set, as the correlation and quality of fits are consistently superior regardless of the cutoff distance. This result is beneficial in that the undamped case is less computationally prohibitive do to the lack of complimentary error function calculation when performing the electrostatic pair interaction. The reaction field results illustrates some of that method's limitations, primarily that it was developed for use in homogenous systems; although it does provide results that are an improvement over those from an unmodified cutoff. |
| 245 |
|
|
| 246 |
< |
While studying the energy differences provides insight into how comparable these methods are energetically, if we want to use these methods in Molecular Dynamics simulations, we also need to consider their effect on forces and torques. Both the magnitude and the direction of the force and torque vectors of each of the bodies in the system can be compared to those observed while using SPME. Analysis of the magnitude of these vectors can be performed in the manner described previously for comparing $\Delta E$ values, only instead of a single value between two system configurations, there is a value for each particle in each configuration. For a system of 1000 water molecules and 40 ions, there are 1040 force vectors and 1000 torque vectors. With 500 configurations, this results in excess of 500,000 data samples for each system type. Figures \ref{frcMag} and \ref{trqMag} respectively show the force and torque vector magnitude results for the accumulated analysis over all the system types. |
| 246 |
> |
\subsection{Magnitudes of the Force and Torque Vectors} |
| 247 |
|
|
| 248 |
+ |
Evaluation of pairwise methods for use in Molecular Dynamics simulations requires consideration of effects on the forces and torques. Investigation of the force and torque vector magnitudes provides a measure of the strength of these values relative to SPME. Figures \ref{fig:frcMag} and \ref{fig:trqMag} respectively show the force and torque vector magnitude regression results for the accumulated analysis over all the system types. |
| 249 |
+ |
|
| 250 |
|
\begin{figure} |
| 251 |
|
\centering |
| 252 |
|
\includegraphics[width=3.25in]{./frcMagplot.pdf} |
| 253 |
< |
\caption{The results from the statistical analysis of the force vector magnitude results for all the system types at 9 \AA\ (${\bullet}$), 12 \AA\ ($\blacksquare$), and 15 \AA\ ($\blacktriangledown$) cutoff radii. Results close to a value of 1 (dashed line) indicate force vector magnitude values from that particular method (listed on the left) are nearly indistinguishable from those obtained from SPME.} |
| 254 |
< |
\label{frcMag} |
| 253 |
> |
\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) indicate force magnitude values indistinguishable from those obtained using SPME. Different values of the cutoff radius are indicated with different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = inverted triangles).} |
| 254 |
> |
\label{fig:frcMag} |
| 255 |
|
\end{figure} |
| 256 |
|
|
| 257 |
< |
The results in figure \ref{frcMag} for the most part parallel those seen in the previous look at the $\Delta E$ results. The unmodified cutoff results are poor, but using group based cutoffs and a switching function provides a improvement much more significant than what was seen with $\Delta E$. Looking at the Shifted Potential sets, the slope and R$^2$ improve with the use of damping to an optimal result of 0.2 \AA $^{-1}$ for the 12 and 15 \AA\ cutoffs. Further increases in damping, while beneficial for simulations with a cutoff radius of 9 \AA\ , is detrimental to simulations with larger cutoff radii. The undamped Shifted Force method gives forces in line with those obtained using SPME, and use of a damping function gives little to no gain. The reaction field results are surprisingly good, considering the poor quality of the fits for the $\Delta E$ results. There is still a considerable degree of scatter in the data, but it correlates well in general. |
| 257 |
> |
Figure \ref{fig:frcMag}, for the most part, parallels the results seen in the previous $\Delta E$ section. The unmodified cutoff results are poor, but using group based cutoffs and a switching function provides a improvement much more significant than what was seen with $\Delta E$. Looking at the Shifted-Potential sets, the slope and $R^2$ improve with the use of damping to an optimal result of 0.2 \AA $^{-1}$ for the 12 and 15 \AA\ cutoffs. Further increases in damping, while beneficial for simulations with a cutoff radius of 9 \AA\ , is detrimental to simulations with larger cutoff radii. The undamped Shifted-Force method gives forces in line with those obtained using SPME, and use of a damping function results in minor improvement. The reaction field results are surprisingly good, considering the poor quality of the fits for the $\Delta E$ results. There is still a considerable degree of scatter in the data, but it correlates well in general. To be fair, we again note that the reaction field calculations do not encompass NaCl crystal and melt systems, so these results are partly biased towards conditions in which the method performs more favorably. |
| 258 |
|
|
| 113 |
– |
\subsection{Torque Magnitude Comparison} |
| 114 |
– |
|
| 259 |
|
\begin{figure} |
| 260 |
|
\centering |
| 261 |
|
\includegraphics[width=3.25in]{./trqMagplot.pdf} |
| 262 |
< |
\caption{The results from the statistical analysis of the torque vector magnitude results for all the system types at 9 \AA\ (${\bullet}$), 12 \AA\ ($\blacksquare$), and 15 \AA\ ($\blacktriangledown$) cutoff radii. Results close to a value of 1 (dashed line) indicate torque vector magnitude values from that particular method (listed on the left) are nearly indistinguishable from those obtained from SPME. Torques are only accumulated on the rigid water molecules, so these results exclude NaCl the systems.} |
| 263 |
< |
\label{trqMag} |
| 262 |
> |
\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) indicate torque magnitude values indistinguishable from those obtained using SPME. Different values of the cutoff radius are indicated with different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = inverted triangles).} |
| 263 |
> |
\label{fig:trqMag} |
| 264 |
|
\end{figure} |
| 265 |
|
|
| 266 |
< |
The torque vector magnitude results in figure \ref{trqMag} are similar to those seen for the forces, but more clearly show the improved behavior with increasing cutoff radius. Moderate damping is beneficial to the Shifted Potential and unnecessary with the Shifted Force method, and they also show that over-damping adversely effects all cutoff radii rather than showing an improvement for systems with short cutoffs. The reaction field method performs well when calculating the torques, better than the Shifted Force method over this limited data set. |
| 266 |
> |
To evaluate the torque vector magnitudes, the data set from which values are drawn is limited to rigid molecules in the systems (i.e. water molecules). In spite of this smaller sampling pool, the torque vector magnitude results in figure \ref{fig:trqMag} are still similar to those seen for the forces; however, they more clearly show the improved behavior that comes with increasing the cutoff radius. Moderate damping is beneficial to the Shifted-Potential and helpful yet possibly unnecessary with the Shifted-Force method, and they also show that over-damping adversely effects all cutoff radii rather than showing an improvement for systems with short cutoffs. The reaction field method performs well when calculating the torques, better than the Shifted Force method over this limited data set. |
| 267 |
|
|
| 268 |
< |
\subsection{Force and Torque Direction Comparison} |
| 268 |
> |
\subsection{Directionality of the Force and Torque Vectors} |
| 269 |
|
|
| 270 |
< |
Having force and torque vectors with magnitudes that are well correlated to SPME is good, but if they are not pointing in the proper direction the results will be incorrect. These vector directions were investigated through measurement of the angle formed between them and those from SPME. The dot product of these unit vectors provides a theta value that is accumulated in a distribution function, weighted by the area on the unit sphere. Narrow distributions of theta values indicates similar to identical results between the tested method and SPME. To measure the narrowness of the resulting distributions, non-linear Gaussian fits were performed. |
| 270 |
> |
Having force and torque vectors with magnitudes that are well correlated to SPME is good, but if they are not pointing in the proper direction the results will be incorrect. These vector directions were investigated through measurement of the angle formed between them and those from SPME. The results (Fig. \ref{fig:frcTrqAng}) are compared through the variance ($\sigma^2$) of the Gaussian fits of the angle error distributions of the combined set over all system types. |
| 271 |
|
|
| 272 |
|
\begin{figure} |
| 273 |
|
\centering |
| 130 |
– |
\includegraphics[width=3.25in]{./gaussFit.pdf} |
| 131 |
– |
\caption{Example fitting of the angular distribution of the force vectors over all of the studied systems. The solid and dotted lines show Gaussian and Voigt fits of the distribution data respectively. Even though the Voigt profile make for a more accurate fit, the Gaussian was used due to more versatile statistical results.} |
| 132 |
– |
\label{gaussian} |
| 133 |
– |
\end{figure} |
| 134 |
– |
|
| 135 |
– |
Figure \ref{gaussian} shows an example distribution and the non-linear fit applied. The solid line is a Gaussian profile, while the dotted line is a Voigt profile, a convolution of a Gaussian and a Lorentzian profile. Since this distribution is a measure of angular error between two different electrostatic summation methods, there is particular reason for it to adhere to a particular shape. Because of this and the Gaussian profile's more statistically meaningful properties, Gaussian fitting was used to compare all the methods considered in this study. The results (Fig. \ref{frcTrqAng}) are compared through the variance ($\sigma^2$) of these non-linear fits. |
| 136 |
– |
|
| 137 |
– |
\begin{figure} |
| 138 |
– |
\centering |
| 274 |
|
\includegraphics[width=3.25in]{./frcTrqAngplot.pdf} |
| 275 |
< |
\caption{The results from the statistical analysis of the force and torque vector angular distributions for all the system types at 9 \AA\ (${\bullet}$), 12 \AA\ ($\blacksquare$), and 15 \AA\ ($\blacktriangledown$) cutoff radii. Plotted values are the variance ($\sigma^2$) of the Gaussian non-linear fits. Results close to a value of 0 (dashed line) indicate force or torque vector directions from that particular method (listed on the left) are nearly indistinguishable from those obtained from SPME. Torques are only accumulated on the rigid water molecules, so the torque vector angle results exclude NaCl the systems.} |
| 276 |
< |
\label{frcTrqAng} |
| 275 |
> |
\caption{Statistical analysis of the quality of the Gaussian fit of the force and torque vector angular distributions for a given electrostatic method compared with the reference Ewald sum. Results with a variance ($\sigma^2$) equal to zero (dashed line) indicate force and torque directions indistinguishable from those obtained using SPME. Different values of the cutoff radius are indicated with different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = inverted triangles).} |
| 276 |
> |
\label{fig:frcTrqAng} |
| 277 |
|
\end{figure} |
| 278 |
|
|
| 279 |
< |
Both the force and torque $\sigma^2$ results from the analysis of the total accumulated system data are tabulated in figure \ref{frcTrqAng}. All of the sets, aside from the over-damped case show the improvement afforded by choosing a longer simulation cutoff. Increasing the cutoff from 9 to 12 \AA\ typically results in a halving of $\sigma^2$, with a similar improvement going from 12 to 15 \AA . The undamped Shifted Force, Group Based Cutoff, and Reaction Field methods all do equivalently well at capturing the direction of both the force and torque vectors. Using damping improves the angular behavior significantly for the Shifted Potential and moderately for the Shifted Force methods. Increasing the damping too far is destructive for both methods, particularly to the torque vectors. Again it is important to recognize that the force vectors cover all particles in the systems, while torque vectors are only available for neutral molecular groups. Damping appears to have a more beneficial non-neutral bodies, and this observation is investigated further in the accompanying supporting information. |
| 279 |
> |
Both the force and torque $\sigma^2$ results from the analysis of the total accumulated system data are tabulated in figure \ref{fig:frcTrqAng}. All of the sets, aside from the over-damped case show the improvement afforded by choosing a longer simulation cutoff. Increasing the cutoff from 9 to 12 \AA\ typically results in a halving of the distribution widths, with a similar improvement going from 12 to 15 \AA . The undamped Shifted-Force, Group Based Cutoff, and Reaction Field methods all do equivalently well at capturing the direction of both the force and torque vectors. Using damping improves the angular behavior significantly for the Shifted-Potential and moderately for the Shifted-Force methods. Increasing the damping too far is destructive for both methods, particularly to the torque vectors. Again it is important to recognize that the force vectors cover all particles in the systems, while torque vectors are only available for neutral molecular groups. Damping appears to have a more beneficial effect on non-neutral bodies, and this observation is investigated further in the accompanying supporting information. |
| 280 |
|
|
| 281 |
|
\begin{table}[htbp] |
| 282 |
|
\centering |
| 308 |
|
|
| 309 |
|
\bottomrule |
| 310 |
|
\end{tabular} |
| 311 |
< |
\label{groupAngle} |
| 311 |
> |
\label{tab:groupAngle} |
| 312 |
|
\end{table} |
| 313 |
|
|
| 314 |
< |
Although not discussed previously, group based cutoffs can be applied to both the Shifted Potential and Force methods. Use off a switching function corrects for the discontinuities that arise when atoms of a group exit the cutoff before the group's center of mass. Though there are no significant benefit or drawbacks observed in $\Delta E$ and vector magnitude results when doing this, there is a measurable improvement in the vector angle results. Table \ref{groupAngle} shows the angular variance values obtained using group based cutoffs and a switching function alongside the standard results seen in figure \ref{frcTrqAng} for comparison purposes. The Shifted Potential shows much narrower angular distributions for both the force and torque vectors when using an $\alpha$ of 0.2 \AA$^{-1}$ or less, while Shifted Force shows improvements in the undamped and lightly damped cases. Thus, by calculating the electrostatic interactions in terms of molecular pairs rather than atomic pairs, the direction of the force and torque vectors are determined more accurately. |
| 314 |
> |
Although not discussed previously, group based cutoffs can be applied to both the Shifted-Potential and Shifted-Force methods. Use off a switching function corrects for the discontinuities that arise when atoms of a group exit the cutoff before the group's center of mass. Though there are no significant benefit or drawbacks observed in $\Delta E$ and vector magnitude results when doing this, there is a measurable improvement in the vector angle results. Table \ref{tab:groupAngle} shows the angular variance values obtained using group based cutoffs and a switching function alongside the standard results seen in figure \ref{fig:frcTrqAng} for comparison purposes. The Shifted-Potential shows much narrower angular distributions for both the force and torque vectors when using an $\alpha$ of 0.2 \AA$^{-1}$ or less, while Shifted-Force shows improvements in the undamped and lightly damped cases. Thus, by calculating the electrostatic interactions in terms of molecular pairs rather than atomic pairs, the direction of the force and torque vectors are determined more accurately. |
| 315 |
|
|
| 316 |
< |
One additional trend to recognize in table \ref{groupAngle} is that the $\sigma^2$ values for both Shifted Potential and Shifted Force converge as $\alpha$ increases, something that is easier to see when using group based cutoffs. Looking back on figures \ref{delE}, \ref{frcMag}, and \ref{trqMag}, show this behavior clearly at large $\alpha$ and cutoff values. The reason for this is that the complimentary error function inserted into the potential weakens the electrostatic interaction as $\alpha$ increases. Thus, at larger values of $\alpha$, both the summation method types progress toward non-interacting functions, so care is required in choosing large damping functions lest one generate an undesirable loss in the pair interaction. Kast \textit{et al.} developed a method for choosing appropriate $\alpha$ values for these types of electrostatic summation methods by fitting to $g(r)$ data, and their methods indicate optimal values of 0.34, 0.25, and 0.16 \AA$^{-1}$ for cutoff values of 9, 12, and 15 \AA\ respectively.\cite{Kast03} These appear to be reasonable choices to obtain proper MC behavior (Fig. \ref{delE}); however, based on these findings, choices this high would be introducing error in the molecular torques, particularly for the shorter cutoffs. Based on the above findings, any empirical damping is arguably unnecessary with the choice of the Shifted Force method. |
| 316 |
> |
One additional trend to recognize in table \ref{tab:groupAngle} is that the $\sigma^2$ values for both Shifted-Potential and Shifted-Force converge as $\alpha$ increases, something that is easier to see when using group based cutoffs. Looking back on figures \ref{fig:delE}, \ref{fig:frcMag}, and \ref{fig:trqMag}, show this behavior clearly at large $\alpha$ and cutoff values. The reason for this is that the complimentary error function inserted into the potential weakens the electrostatic interaction as $\alpha$ increases. Thus, at larger values of $\alpha$, both the summation method types progress toward non-interacting functions, so care is required in choosing large damping functions lest one generate an undesirable loss in the pair interaction. Kast \textit{et al.} developed a method for choosing appropriate $\alpha$ values for these types of electrostatic summation methods by fitting to $g(r)$ data, and their methods indicate optimal values of 0.34, 0.25, and 0.16 \AA$^{-1}$ for cutoff values of 9, 12, and 15 \AA\ respectively.\cite{Kast03} These appear to be reasonable choices to obtain proper MC behavior (Fig. \ref{fig:delE}); however, based on these findings, choices this high would introduce error in the molecular torques, particularly for the shorter cutoffs. Based on the above findings, empirical damping up to 0.2 \AA$^{-1}$ proves to be beneficial, but damping is arguably unnecessary when using the Shifted-Force method. |
| 317 |
|
|
| 318 |
+ |
\subsection{Collective Motion: Power Spectra of NaCl Crystals} |
| 319 |
+ |
|
| 320 |
+ |
In the previous studies using a Shifted-Force variant of the damped Wolf coulomb potential, the structure and dynamics of water were investigated rather extensively.\cite{Zahn02,Kast03} Their results indicated that the damped Shifted-Force method results in properties very similar to those obtained when using the Ewald summation. Considering the statistical results shown above, the good performance of this method is not that surprising. Rather than consider the same systems and simply recapitulate their results, we decided to look at the solid state dynamical behavior obtained using the best performing summation methods from the above results. |
| 321 |
+ |
|
| 322 |
+ |
\begin{figure} |
| 323 |
+ |
\centering |
| 324 |
+ |
\includegraphics[width = 3.25in]{./spectraSquare.pdf} |
| 325 |
+ |
\caption{Power spectra obtained from the velocity auto-correlation functions of NaCl crystals at 1000 K while using SPME, Shifted-Force ($\alpha$ = 0, 0.1, \& 0.2), and Shifted-Potential ($\alpha$ = 0.2). Apodization of the correlation functions via a cubic switching function between 40 and 50 ps was used to clear up the spectral noise resulting from data truncation, and had no noticeable effect on peak location or magnitude. The inset shows the frequency region below 100 cm$^{-1}$ to highlight where the spectra begin to differentiate.} |
| 326 |
+ |
\label{fig:methodPS} |
| 327 |
+ |
\end{figure} |
| 328 |
+ |
|
| 329 |
+ |
Figure \ref{fig:methodPS} shows the power spectra for the NaCl crystals (from averaged Na and Cl ion velocity autocorrelation functions) using the stated electrostatic summation methods. While high frequency peaks of all the spectra overlap, showing the same general features, the low frequency region shows how the summation methods differ. Considering the low-frequency inset (expanded in the upper frame of figure \ref{fig:dampInc}), at frequencies below 100 cm$^{-1}$, the correlated motions are blue-shifted when using undamped or weakly damped Shifted-Force. When using moderate damping ($\alpha = 0.2$ \AA$^{-1}$) both the Shifted-Force and Shifted-Potential methods give near identical correlated motion behavior as the Ewald method (which has a damping value of 0.3119). The damping acts as a distance dependent Gaussian screening of the point charges for the pairwise summation methods. This weakening of the electrostatic interaction with distance explains why the long-ranged correlated motions are at lower frequencies for the moderately damped methods than for undamped or weakly damped methods. To see this effect more clearly, we show how damping strength affects a simple real-space electrostatic potential, |
| 330 |
+ |
\begin{equation} |
| 331 |
+ |
V_\textrm{damped}=\sum^N_i\sum^N_{j\ne i}q_iq_j\left[\frac{\textrm{erfc}({\alpha r_{ij}})}{r_{ij}}\right]S(r), |
| 332 |
+ |
\end{equation} |
| 333 |
+ |
where $S(r)$ is a switching function that smoothly zeroes the potential at the cutoff radius. Figure \ref{fig:dampInc} shows how the low frequency motions are dependent on the damping used in the direct electrostatic sum. As the damping increases, the peaks drop to lower frequencies. Incidentally, use of an $\alpha$ of 0.25 \AA$^{-1}$ on a simple electrostatic summation results in low frequency correlated dynamics equivalent to a simulation using SPME. When the coefficient lowers to 0.15 \AA$^{-1}$ and below, these peaks shift to higher frequency in exponential fashion. Though not shown, the spectrum for the simple undamped electrostatic potential is blue-shifted such that the lowest frequency peak resides near 325 cm$^{-1}$. In light of these results, the undamped Shifted-Force method producing low-lying motion peaks within 10 cm$^{-1}$ of SPME is quite respectable; however, it appears as though moderate damping is required for accurate reproduction of crystal dynamics. |
| 334 |
+ |
\begin{figure} |
| 335 |
+ |
\centering |
| 336 |
+ |
\includegraphics[width = 3.25in]{./comboSquare.pdf} |
| 337 |
+ |
\caption{Upper: Zoomed inset from figure \ref{fig:methodPS}. As the damping value for the Shifted-Force potential increases, the low-frequency peaks red-shift. Lower: Low-frequency correlated motions for NaCl crystals at 1000 K when using SPME and a simple damped Coulombic sum with damping coefficients ($\alpha$) ranging from 0.15 to 0.3 \AA$^{-1}$. As $\alpha$ increases, the peaks are red-shifted toward and eventually beyond the values given by SPME. The larger $\alpha$ values weaken the real-space electrostatics, explaining this shift towards less strongly correlated motions in the crystal.} |
| 338 |
+ |
\label{fig:dampInc} |
| 339 |
+ |
\end{figure} |
| 340 |
+ |
|
| 341 |
|
\section{Conclusions} |
| 342 |
|
|
| 343 |
+ |
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 as equation \ref{eq:SFPot}, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. The cumulative energy difference results showed the undamped Shifted-Force and moderately damped Shifted-Potential methods produced results nearly identical to SPME. Similarly for the dynamic features, the undamped or moderately damped Shifted-Force and moderately damped Shifted-Potential methods produce force and torque vector magnitude and directions very similar to the expected values. These results translate into long-time dynamic behavior equivalent to that produced in simulations using SPME. |
| 344 |
+ |
|
| 345 |
+ |
Aside from the computational cost benefit, these techniques have applicability in situations where the use of the Ewald sum can prove problematic. Primary among them is their use in interfacial systems, where the unmodified lattice sum techniques artificially accentuate the periodicity of the system in an undesirable manner. There have been alterations to the standard Ewald techniques, via corrections and reformulations, to compensate for these systems; but the pairwise techniques discussed here require no modifications, making them natural tools to tackle these problems. Additionally, this transferability gives them benefits over other pairwise methods, like reaction field, because estimations of physical properties (e.g. the dielectric constant) are unnecessary. |
| 346 |
+ |
|
| 347 |
+ |
We are not suggesting any flaw with the Ewald sum; in fact, it is the standard by which these simple pairwise sums are judged. However, these results do suggest that in the typical simulations performed today, the Ewald summation may no longer be required to obtain the level of accuracy most researcher have come to expect |
| 348 |
+ |
|
| 349 |
|
\section{Acknowledgments} |
| 350 |
|
|
| 351 |
|
\newpage |
