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\chapter{\label{chap:electrostatics}ELECTROSTATIC INTERACTION CORRECTION |
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TECHNIQUES} |
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|
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In molecular simulations, proper accumulation of the electrostatic |
5 |
interactions is essential and is one of the most |
6 |
computationally-demanding tasks. The common molecular mechanics force |
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fields represent atomic sites with full or partial charges protected |
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by Lennard-Jones (short range) interactions. This means that nearly |
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every pair interaction involves a calculation of charge-charge forces. |
10 |
Coupled with relatively long-ranged $r^{-1}$ decay, the monopole |
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interactions quickly become the most expensive part of molecular |
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simulations. Historically, the electrostatic pair interaction would |
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not have decayed appreciably within the typical box lengths that could |
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be feasibly simulated. In the larger systems that are more typical of |
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modern simulations, large cutoffs should be used to incorporate |
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electrostatics correctly. |
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|
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There have been many efforts to address the proper and practical |
19 |
handling of electrostatic interactions, and these have resulted in a |
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variety of techniques.\cite{Roux99,Sagui99,Tobias01} These are |
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typically classified as implicit methods (i.e., continuum dielectrics, |
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static dipolar fields),\cite{Born20,Grossfield00} explicit methods |
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(i.e., Ewald summations, interaction shifting or |
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truncation),\cite{Ewald21,Steinbach94} or a mixture of the two (i.e., |
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reaction field type methods, fast multipole |
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methods).\cite{Onsager36,Rokhlin85} The explicit or mixed methods are |
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often preferred because they physically incorporate solvent molecules |
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in the system of interest, but these methods are sometimes difficult |
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to utilize because of their high computational cost.\cite{Roux99} In |
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addition to the computational cost, there have been some questions |
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regarding possible artifacts caused by the inherent periodicity of the |
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explicit Ewald summation.\cite{Tobias01} |
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|
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In this chapter, we focus on a new set of pairwise methods devised by |
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Wolf {\it et al.},\cite{Wolf99} which we further extend. These |
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methods along with a few other mixed methods (i.e. reaction field) are |
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compared with the smooth particle mesh Ewald |
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sum,\cite{Onsager36,Essmann99} which is our reference method for |
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handling long-range electrostatic interactions. The new methods for |
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handling electrostatics have the potential to scale linearly with |
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increasing system size since they involve only a simple modification |
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to the direct pairwise sum. They also lack the added periodicity of |
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the Ewald sum, so they can be used for systems which are non-periodic |
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or which have one- or two-dimensional periodicity. Below, these |
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methods are evaluated using a variety of model systems to |
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establish their usability in molecular simulations. |
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|
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\section{The Ewald Sum} |
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|
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The complete accumulation of the electrostatic interactions in a system with |
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periodic boundary conditions (PBC) requires the consideration of the |
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effect of all charges within a (cubic) simulation box as well as those |
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in the periodic replicas, |
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\begin{equation} |
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V_\textrm{elec} = \frac{1}{2} {\sum_{\mathbf{n}}}^\prime |
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\left[ \sum_{i=1}^N\sum_{j=1}^N \phi |
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\left( \mathbf{r}_{ij} + L\mathbf{n},\bm{\Omega}_i,\bm{\Omega}_j\right) |
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\right], |
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\label{eq:PBCSum} |
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\end{equation} |
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where the sum over $\mathbf{n}$ is a sum over all periodic box |
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replicas with integer coordinates $\mathbf{n} = (l,m,n)$, and the |
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prime indicates $i = j$ are neglected for $\mathbf{n} = |
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0$.\cite{deLeeuw80} Within the sum, $N$ is the number of electrostatic |
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particles, $\mathbf{r}_{ij}$ is $\mathbf{r}_j - \mathbf{r}_i$, $L$ is |
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the cell length, $\bm{\Omega}_{i,j}$ are the Euler angles for $i$ and |
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$j$, and $\phi$ is the solution to Poisson's equation |
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($\phi(\mathbf{r}_{ij}) = q_i q_j |\mathbf{r}_{ij}|^{-1}$ for |
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charge-charge interactions). In the case of monopole electrostatics, |
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equation (\ref{eq:PBCSum}) is conditionally convergent and is divergent for |
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non-neutral systems. |
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|
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The electrostatic summation problem was originally studied by Ewald |
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for the case of an infinite crystal.\cite{Ewald21}. The approach he |
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took was to convert this conditionally convergent sum into two |
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absolutely convergent summations: a short-ranged real-space summation |
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and a long-ranged reciprocal-space summation, |
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\begin{equation} |
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\begin{split} |
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V_\textrm{elec} = \frac{1}{2}& |
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\sum_{i=1}^N\sum_{j=1}^N \Biggr[ q_i q_j\Biggr( {\sum_{\mathbf{n}}}^\prime |
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\frac{\textrm{erfc}\left( \alpha|\mathbf{r}_{ij}+\mathbf{n}|\right)} |
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{|\mathbf{r}_{ij}+\mathbf{n}|} \\ |
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&+ \frac{1}{\pi L^3}\sum_{\mathbf{k}\ne 0}\frac{4\pi^2}{|\mathbf{k}|^2} |
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\exp{\left(-\frac{\pi^2|\mathbf{k}|^2}{\alpha^2}\right) |
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\cos\left(\mathbf{k}\cdot\mathbf{r}_{ij}\right)}\Biggr)\Biggr] \\ |
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&- \frac{\alpha}{\pi^{1/2}}\sum_{i=1}^N q_i^2 |
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+ \frac{2\pi}{(2\epsilon_\textrm{S}+1)L^3} |
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\left|\sum_{i=1}^N q_i\mathbf{r}_i\right|^2, |
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\end{split} |
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\label{eq:EwaldSum} |
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\end{equation} |
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where $\alpha$ is the damping or convergence parameter with units of |
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\AA$^{-1}$, $\mathbf{k}$ are the reciprocal vectors and are equal to |
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$2\pi\mathbf{n}/L^2$, and $\epsilon_\textrm{S}$ is the dielectric |
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constant of the surrounding medium. The final two terms of |
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equation (\ref{eq:EwaldSum}) are a particle-self term and a dipolar term |
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for interacting with a surrounding dielectric.\cite{Allen87} This |
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dipolar term was neglected in early applications in molecular |
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simulations,\cite{Brush66,Woodcock71} until it was introduced by de |
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Leeuw {\it et al.} to address situations where the unit cell has a |
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dipole moment which is magnified through replication of the periodic |
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images.\cite{deLeeuw80,Smith81} If this term is taken to be zero, the |
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system is said to be using conducting (or ``tin-foil'') boundary |
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conditions, $\epsilon_{\rm S} = \infty$. Figure |
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\ref{fig:ewaldTime} shows how the Ewald sum has been applied over |
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time. Initially, due to the small system sizes that could be |
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simulated feasibly, the entire simulation box was replicated to |
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convergence. In more modern simulations, the systems have grown large |
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enough that a real-space cutoff could potentially give convergent |
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behavior. Indeed, it has been observed that with the choice of a |
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small $\alpha$, the reciprocal-space portion of the Ewald sum can be |
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rapidly convergent and small relative to the real-space |
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portion.\cite{Karasawa89,Kolafa92} |
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|
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\begin{figure} |
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\includegraphics[width=\linewidth]{./figures/ewaldProgression.pdf} |
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\caption{The change in the need for the Ewald sum with |
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increasing computational power. A:~Initially, only small systems |
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could be studied, and the Ewald sum replicated the simulation box to |
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convergence. B:~Now, radial cutoff methods should be able to reach |
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convergence for the larger systems of charges that are common today.} |
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\label{fig:ewaldTime} |
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\end{figure} |
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|
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The original Ewald summation is an $\mathscr{O}(N^2)$ algorithm. The |
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convergence parameter $(\alpha)$ plays an important role in balancing |
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the computational cost between the direct and reciprocal-space |
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portions of the summation. The choice of this value allows one to |
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select whether the real-space or reciprocal space portion of the |
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summation is an $\mathscr{O}(N^2)$ calculation (with the other being |
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$\mathscr{O}(N)$).\cite{Sagui99} With the appropriate choice of |
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$\alpha$ and thoughtful algorithm development, this cost can be |
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reduced to $\mathscr{O}(N^{3/2})$.\cite{Perram88} The typical route |
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taken to reduce the cost of the Ewald summation even further is to set |
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$\alpha$ such that the real-space interactions decay rapidly, allowing |
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for a short spherical cutoff. Then the reciprocal space summation is |
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optimized. These optimizations usually involve utilization of the |
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fast Fourier transform (FFT),\cite{Hockney81} leading to the |
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particle-particle particle-mesh (P3M) and particle mesh Ewald (PME) |
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methods.\cite{Shimada93,Luty94,Luty95,Darden93,Essmann95} In these |
142 |
methods, the cost of the reciprocal-space portion of the Ewald |
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summation is reduced from $\mathscr{O}(N^2)$ down to $\mathscr{O}(N |
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\log N)$. |
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|
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These developments and optimizations have made the use of the Ewald |
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summation routine in simulations with periodic boundary |
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conditions. However, in certain systems, such as vapor-liquid |
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interfaces and membranes, the intrinsic three-dimensional periodicity |
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can prove problematic. The Ewald sum has been reformulated to handle |
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2-D systems,\cite{Parry75,Parry76,Heyes77,deLeeuw79,Rhee89} but these |
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methods are computationally expensive.\cite{Spohr97,Yeh99} More |
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recently, there have been several successful efforts toward reducing |
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the computational cost of 2-D lattice |
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summations,\cite{Yeh99,Kawata01,Arnold02,deJoannis02,Brodka04} |
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bringing them more in line with the cost of the full 3-D summation. |
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|
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Several studies have recognized that the inherent periodicity in the |
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Ewald sum can also have an effect on three-dimensional |
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systems.\cite{Roberts94,Roberts95,Luty96,Hunenberger99a,Hunenberger99b,Weber00} |
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Solvated proteins are essentially kept at high concentration due to |
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the periodicity of the electrostatic summation method. In these |
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systems, the more compact folded states of a protein can be |
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artificially stabilized by the periodic replicas introduced by the |
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Ewald summation.\cite{Weber00} Thus, care must be taken when |
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considering the use of the Ewald summation where the assumed |
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periodicity would introduce spurious effects in the system dynamics. |
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|
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|
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\section{The Wolf and Zahn Methods} |
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|
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In a recent paper by Wolf \textit{et al.}, a procedure was outlined |
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for the accurate accumulation of electrostatic interactions in an |
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efficient pairwise fashion. This procedure lacks the inherent |
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periodicity of the Ewald summation.\cite{Wolf99} Wolf \textit{et al.} |
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observed that the electrostatic interaction is effectively |
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short-ranged in condensed phase systems and that neutralization of the |
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charge contained within the cutoff radius is crucial for potential |
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stability. They devised a pairwise summation method that ensures |
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charge neutrality and gives results similar to those obtained with the |
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Ewald summation. The resulting shifted Coulomb potential includes |
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image-charges subtracted out through placement on the cutoff sphere |
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and a distance-dependent damping function (identical to that seen in |
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the real-space portion of the Ewald sum) to aid convergence |
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\begin{equation} |
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V_{\textrm{Wolf}}(r_{ij})= \frac{q_i q_j \textrm{erfc}(\alpha r_{ij})}{r_{ij}} |
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- \lim_{r_{ij}\rightarrow R_\textrm{c}} |
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\left\{\frac{q_iq_j \textrm{erfc}(\alpha r_{ij})}{r_{ij}}\right\}. |
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\label{eq:WolfPot} |
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\end{equation} |
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Equation (\ref{eq:WolfPot}) is essentially the common form of a shifted |
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potential. However, neutralizing the charge contained within each |
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cutoff sphere requires the placement of a self-image charge on the |
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surface of the cutoff sphere. This additional self-term in the total |
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potential enabled Wolf {\it et al.} to obtain excellent estimates of |
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Madelung energies for many crystals. |
197 |
|
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In order to use their charge-neutralized potential in molecular |
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dynamics simulations, Wolf \textit{et al.} suggested taking the |
200 |
derivative of this potential prior to evaluation of the limit. This |
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procedure gives an expression for the forces, |
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\begin{equation} |
203 |
\begin{split} |
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F_{\textrm{Wolf}}(r_{ij}) = q_i q_j \Biggr\{& |
205 |
\Biggr[\frac{\textrm{erfc}\left(\alpha r_{ij}\right)}{r^2_{ij}} |
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+ \frac{2\alpha}{\pi^{1/2}}\frac{\exp{\left(-\alpha^2r_{ij}^2\right)}}{r_{ij}} |
207 |
\Biggr]\\ |
208 |
&-\Biggr[ |
209 |
\frac{\textrm{erfc}\left(\alpha R_{\textrm{c}}\right)}{R_{\textrm{c}}^2} |
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+ \frac{2\alpha}{\pi^{1/2}} |
211 |
\frac{\exp{\left(-\alpha^2R_{\textrm{c}}^2\right)}}{R_{\textrm{c}}} |
212 |
\Biggr]\Biggr\}, |
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\end{split} |
214 |
\label{eq:WolfForces} |
215 |
\end{equation} |
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that incorporates both image charges and damping of the electrostatic |
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interaction. |
218 |
|
219 |
More recently, Zahn \textit{et al.} investigated these potential and |
220 |
force expressions for use in simulations involving water.\cite{Zahn02} |
221 |
In their work, they pointed out that the forces and derivative of |
222 |
the potential are not commensurate. Attempts to use both |
223 |
equations (\ref{eq:WolfPot}) and (\ref{eq:WolfForces}) together will lead |
224 |
to poor energy conservation. They correctly observed that taking the |
225 |
limit shown in equation (\ref{eq:WolfPot}) {\it after} calculating the |
226 |
derivatives gives forces for a different potential energy function |
227 |
than the one shown in equation (\ref{eq:WolfPot}). |
228 |
|
229 |
Zahn \textit{et al.} introduced a modified form of this summation |
230 |
method as a way to use the technique in Molecular Dynamics |
231 |
simulations. They proposed a new damped Coulomb potential, |
232 |
\begin{equation} |
233 |
\begin{split} |
234 |
V_{\textrm{Zahn}}(r_{ij}) = q_iq_j\Biggr\{& |
235 |
\frac{\mathrm{erfc}\left(\alpha r_{ij}\right)}{r_{ij}} \\ |
236 |
&- \left[\frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}^2} |
237 |
+ \frac{2\alpha}{\pi^{1/2}} |
238 |
\frac{\exp\left(-\alpha^2R_\mathrm{c}^2\right)}{R_\mathrm{c}} |
239 |
\right]\left(r_{ij}-R_\mathrm{c}\right)\Biggr\}, |
240 |
\end{split} |
241 |
\label{eq:ZahnPot} |
242 |
\end{equation} |
243 |
and showed that this potential does fairly well at capturing the |
244 |
structural and dynamic properties of water compared the same |
245 |
properties obtained using the Ewald sum. |
246 |
|
247 |
\section{Simple Forms for Pairwise Electrostatics}\label{sec:PairwiseDerivation} |
248 |
|
249 |
The potentials proposed by Wolf \textit{et al.} and Zahn \textit{et |
250 |
al.} are constructed using two different (and separable) computational |
251 |
tricks: |
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|
253 |
\begin{enumerate}[itemsep=0pt] |
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\item shifting through the use of image charges, and |
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\item damping the electrostatic interaction. |
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\end{enumerate} |
257 |
Wolf \textit{et al.} treated the development of their summation method |
258 |
as a progressive application of these techniques,\cite{Wolf99} while |
259 |
Zahn \textit{et al.} founded their damped Coulomb modification |
260 |
(Eq. (\ref{eq:ZahnPot})) on the post-limit forces |
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(Eq. (\ref{eq:WolfForces})) which were derived using both techniques. |
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It is possible, however, to separate these tricks and study their |
263 |
effects independently. |
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|
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Starting with the original observation that the effective range of the |
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electrostatic interaction in condensed phases is considerably less |
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than $r^{-1}$, either the cutoff sphere neutralization or the |
268 |
distance-dependent damping technique could be used as a foundation for |
269 |
a new pairwise summation method. Wolf \textit{et al.} made the |
270 |
observation that charge neutralization within the cutoff sphere plays |
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a significant role in energy convergence; therefore we will begin our |
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analysis with the various shifted forms that maintain this charge |
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neutralization. We can evaluate the methods of Wolf {\it et al.} and |
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Zahn {\it et al.} by considering the standard shifted potential, |
275 |
\begin{equation} |
276 |
V_\textrm{SP}(r) = \begin{cases} |
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v(r)-v_\textrm{c} &\quad r\leqslant R_\textrm{c} \\ 0 &\quad r > |
278 |
R_\textrm{c} |
279 |
\end{cases}, |
280 |
\label{eq:shiftingPotForm} |
281 |
\end{equation} |
282 |
and shifted force, |
283 |
\begin{equation} |
284 |
V_\textrm{SF}(r) = \begin{cases} |
285 |
v(r) - v_\textrm{c} |
286 |
- \left(\frac{d v(r)}{d r}\right)_{r=R_\textrm{c}}(r-R_\textrm{c}) |
287 |
&\quad r\leqslant R_\textrm{c} \\ 0 &\quad r > R_\textrm{c} |
288 |
\end{cases}, |
289 |
\label{eq:shiftingForm} |
290 |
\end{equation} |
291 |
functions where $v(r)$ is the unshifted form of the potential, and |
292 |
$v_c$ is $v(R_\textrm{c})$. The Shifted Force ({\sc sf}) form ensures |
293 |
that both the potential and the forces goes to zero at the cutoff |
294 |
radius, while the Shifted Potential ({\sc sp}) form only ensures the |
295 |
potential is smooth at the cutoff radius |
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($R_\textrm{c}$).\cite{Allen87} |
297 |
|
298 |
The forces associated with the shifted potential are simply the forces |
299 |
of the unshifted potential itself (when inside the cutoff sphere), |
300 |
\begin{equation} |
301 |
F_{\textrm{SP}} = -\left( \frac{d v(r)}{dr} \right), |
302 |
\end{equation} |
303 |
and are zero outside. Inside the cutoff sphere, the forces associated |
304 |
with the shifted force form can be written, |
305 |
\begin{equation} |
306 |
F_{\textrm{SF}} = -\left( \frac{d v(r)}{dr} \right) + \left(\frac{d |
307 |
v(r)}{dr} \right)_{r=R_\textrm{c}}. |
308 |
\end{equation} |
309 |
|
310 |
If the potential, $v(r)$, is taken to be the normal Coulomb potential, |
311 |
\begin{equation} |
312 |
v(r) = \frac{q_i q_j}{r}, |
313 |
\label{eq:Coulomb} |
314 |
\end{equation} |
315 |
then the Shifted Potential ({\sc sp}) forms will give Wolf {\it et |
316 |
al.}'s undamped prescription: |
317 |
\begin{equation} |
318 |
V_\textrm{SP}(r) = |
319 |
q_iq_j\left(\frac{1}{r}-\frac{1}{R_\textrm{c}}\right) \quad |
320 |
r\leqslant R_\textrm{c}, |
321 |
\label{eq:SPPot} |
322 |
\end{equation} |
323 |
with associated forces, |
324 |
\begin{equation} |
325 |
F_\textrm{SP}(r) = q_iq_j\left(\frac{1}{r^2}\right) |
326 |
\quad r\leqslant R_\textrm{c}. |
327 |
\label{eq:SPForces} |
328 |
\end{equation} |
329 |
These forces are identical to the forces of the standard Coulomb |
330 |
interaction, and cutting these off at $R_c$ was addressed by Wolf |
331 |
\textit{et al.} as undesirable. They pointed out that the effect of |
332 |
the image charges is neglected in the forces when this form is |
333 |
used,\cite{Wolf99} thereby eliminating any benefit from the method in |
334 |
molecular dynamics. Additionally, there is a discontinuity in the |
335 |
forces at the cutoff radius which results in energy drift during MD |
336 |
simulations. |
337 |
|
338 |
The shifted force ({\sc sf}) form using the normal Coulomb potential |
339 |
will give, |
340 |
\begin{equation} |
341 |
V_\textrm{SF}(r) = q_iq_j\left[\frac{1}{r}-\frac{1}{R_\textrm{c}} |
342 |
+ \left(\frac{1}{R_\textrm{c}^2}\right)(r-R_\textrm{c})\right] |
343 |
\quad r\leqslant R_\textrm{c}. |
344 |
\label{eq:SFPot} |
345 |
\end{equation} |
346 |
with associated forces, |
347 |
\begin{equation} |
348 |
F_\textrm{SF}(r) = q_iq_j\left(\frac{1}{r^2}-\frac{1}{R_\textrm{c}^2}\right) |
349 |
\quad r\leqslant R_\textrm{c}. |
350 |
\label{eq:SFForces} |
351 |
\end{equation} |
352 |
This formulation has the benefits that there are no discontinuities at |
353 |
the cutoff radius, while the neutralizing image charges are present in |
354 |
both the energy and force expressions. It would be simple to add the |
355 |
self-neutralizing term back when computing the total energy of the |
356 |
system, thereby maintaining the agreement with the Madelung energies. |
357 |
A side effect of this treatment is the alteration in the shape of the |
358 |
potential that comes from the derivative term. Thus, a degree of |
359 |
clarity about agreement with the empirical potential is lost in order |
360 |
to gain functionality in dynamics simulations. |
361 |
|
362 |
Wolf \textit{et al.} originally discussed the energetics of the |
363 |
shifted Coulomb potential (Eq. \ref{eq:SPPot}) and found that it was |
364 |
insufficient for accurate determination of the energy with reasonable |
365 |
cutoff distances. The calculated Madelung energies fluctuated around |
366 |
the expected value as the cutoff radius was increased, but the |
367 |
oscillations converged toward the correct value.\cite{Wolf99} A |
368 |
damping function was incorporated to accelerate the convergence; and |
369 |
though alternative forms for the damping function could be |
370 |
used,\cite{Jones56,Heyes81} the complimentary error function was |
371 |
chosen to mirror the effective screening used in the Ewald summation. |
372 |
Incorporating this error function damping into the simple Coulomb |
373 |
potential, |
374 |
\begin{equation} |
375 |
v(r) = \frac{\mathrm{erfc}\left(\alpha r\right)}{r}, |
376 |
\label{eq:dampCoulomb} |
377 |
\end{equation} |
378 |
the shifted potential (Eq. (\ref{eq:SPPot})) becomes |
379 |
\begin{equation} |
380 |
V_{\textrm{DSP}}(r) = q_iq_j\left(\frac{\textrm{erfc}\left(\alpha r\right)}{r} |
381 |
- \frac{\textrm{erfc}\left(\alpha R_\textrm{c}\right)}{R_\textrm{c}}\right) |
382 |
\quad r\leqslant R_\textrm{c}, |
383 |
\label{eq:DSPPot} |
384 |
\end{equation} |
385 |
with associated forces, |
386 |
\begin{equation} |
387 |
F_{\textrm{DSP}}(r) = q_iq_j |
388 |
\left(\frac{\textrm{erfc}\left(\alpha r\right)}{r^2} |
389 |
+ \frac{2\alpha}{\pi^{1/2}}\frac{\exp{\left(-\alpha^2r^2\right)}}{r}\right) |
390 |
\quad r\leqslant R_\textrm{c}. |
391 |
\label{eq:DSPForces} |
392 |
\end{equation} |
393 |
Again, this damped shifted potential suffers from a |
394 |
force-discontinuity at the cutoff radius, and the image charges play |
395 |
no role in the forces. To remedy these concerns, one may derive a |
396 |
{\sc sf} variant by including the derivative term in |
397 |
equation (\ref{eq:shiftingForm}), |
398 |
\begin{equation} |
399 |
\begin{split} |
400 |
V_\mathrm{DSF}(r) = q_iq_j\Biggr{[}& |
401 |
\frac{\mathrm{erfc}\left(\alpha r\right)}{r} |
402 |
- \frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}} \\ |
403 |
&+ \left(\frac{\mathrm{erfc}\left(\alpha R_\mathrm{c}\right)}{R_\mathrm{c}^2} |
404 |
+ \frac{2\alpha}{\pi^{1/2}} |
405 |
\frac{\exp\left(-\alpha^2R_\mathrm{c}^2\right)}{R_\mathrm{c}} |
406 |
\right)\left(r-R_\mathrm{c}\right)\ \Biggr{]} |
407 |
\quad r\leqslant R_\textrm{c}. |
408 |
\label{eq:DSFPot} |
409 |
\end{split} |
410 |
\end{equation} |
411 |
The derivative of the above potential will lead to the following forces, |
412 |
\begin{equation} |
413 |
\begin{split} |
414 |
F_\mathrm{DSF}(r) = q_iq_j\Biggr{[}& |
415 |
\left(\frac{\textrm{erfc}\left(\alpha r\right)}{r^2} |
416 |
+ \frac{2\alpha}{\pi^{1/2}}\frac{\exp{\left(-\alpha^2r^2\right)}}{r}\right) \\ |
417 |
&- \left(\frac{\textrm{erfc}\left(\alpha R_{\textrm{c}}\right)} |
418 |
{R_{\textrm{c}}^2} |
419 |
+ \frac{2\alpha}{\pi^{1/2}} |
420 |
\frac{\exp{\left(-\alpha^2R_{\textrm{c}}^2\right)}}{R_{\textrm{c}}} |
421 |
\right)\Biggr{]} |
422 |
\quad r\leqslant R_\textrm{c}. |
423 |
\label{eq:DSFForces} |
424 |
\end{split} |
425 |
\end{equation} |
426 |
If the damping parameter $(\alpha)$ is set to zero, the undamped case, |
427 |
equations (\ref{eq:SPPot} through \ref{eq:SFForces}) are correctly |
428 |
recovered from equations (\ref{eq:DSPPot} through \ref{eq:DSFForces}). |
429 |
|
430 |
This new {\sc sf} potential is similar to equation \ref{eq:ZahnPot} |
431 |
derived by Zahn \textit{et al.}; however, there are two important |
432 |
differences.\cite{Zahn02} First, the $v_\textrm{c}$ term from equation |
433 |
(\ref{eq:shiftingForm}) is equal to equation (\ref{eq:dampCoulomb}) |
434 |
with $r$ replaced by $R_\textrm{c}$. This term is {\it not} present |
435 |
in the Zahn potential, resulting in a potential discontinuity as |
436 |
particles cross $R_\textrm{c}$. Second, the sign of the derivative |
437 |
portion is different. The missing $v_\textrm{c}$ term would not |
438 |
affect molecular dynamics simulations (although the computed energy |
439 |
would be expected to have sudden jumps as particle distances crossed |
440 |
$R_c$). The sign problem is a potential source of errors, however. |
441 |
In fact, it introduces a discontinuity in the forces at the cutoff, |
442 |
because the force function is shifted in the wrong direction and |
443 |
doesn't cross zero at $R_\textrm{c}$. |
444 |
|
445 |
Equations (\ref{eq:DSFPot}) and (\ref{eq:DSFForces}) result in an |
446 |
electrostatic summation method in which the potential and forces are |
447 |
continuous at the cutoff radius and which incorporates the damping |
448 |
function proposed by Wolf \textit{et al.}\cite{Wolf99} In the rest of |
449 |
this paper, we will evaluate exactly how good these methods ({\sc sp}, |
450 |
{\sc sf}, damping) are at reproducing the correct electrostatic |
451 |
summation performed by the Ewald sum. |
452 |
|
453 |
|
454 |
\section{Evaluating Pairwise Summation Techniques} |
455 |
|
456 |
In classical molecular mechanics simulations, there are two primary |
457 |
techniques utilized to obtain information about the system of |
458 |
interest: Monte Carlo (MC) and Molecular Dynamics (MD). Both of these |
459 |
techniques utilize pairwise summations of interactions between |
460 |
particle sites, but they use these summations in different ways. |
461 |
|
462 |
In MC, the potential energy difference between configurations dictates |
463 |
the progression of MC sampling. Going back to the origins of this |
464 |
method, the acceptance criterion for the canonical ensemble laid out |
465 |
by Metropolis \textit{et al.} states that a subsequent configuration |
466 |
is accepted if $\Delta E < 0$ or if $\xi < \exp(-\Delta E/kT)$, where |
467 |
$\xi$ is a random number between 0 and 1.\cite{Metropolis53} |
468 |
Maintaining the correct $\Delta E$ when using an alternate method for |
469 |
handling the long-range electrostatics will ensure proper sampling |
470 |
from the ensemble. |
471 |
|
472 |
In MD, the derivative of the potential governs how the system will |
473 |
progress in time. Consequently, the force and torque vectors on each |
474 |
body in the system dictate how the system evolves. If the magnitude |
475 |
and direction of these vectors are similar when using alternate |
476 |
electrostatic summation techniques, the dynamics in the short term |
477 |
will be indistinguishable. Because error in MD calculations is |
478 |
cumulative, one should expect greater deviation at longer times, |
479 |
although methods which have large differences in the force and torque |
480 |
vectors will diverge from each other more rapidly. |
481 |
|
482 |
\subsection{Monte Carlo and the Energy Gap}\label{sec:MCMethods} |
483 |
|
484 |
The pairwise summation techniques (outlined in section |
485 |
\ref{sec:ESMethods}) were evaluated for use in MC simulations by |
486 |
studying the energy differences between conformations. We took the |
487 |
{\sc spme}-computed energy difference between two conformations to be the |
488 |
correct behavior. An ideal performance by an alternative method would |
489 |
reproduce these energy differences exactly (even if the absolute |
490 |
energies calculated by the methods are different). Since none of the |
491 |
methods provide exact energy differences, we used linear least squares |
492 |
regressions of energy gap data to evaluate how closely the methods |
493 |
mimicked the Ewald energy gaps. Unitary results for both the |
494 |
correlation (slope) and correlation coefficient for these regressions |
495 |
indicate perfect agreement between the alternative method and {\sc spme}. |
496 |
Sample correlation plots for two alternate methods are shown in |
497 |
Fig. \ref{fig:linearFit}. |
498 |
|
499 |
\begin{figure} |
500 |
\centering |
501 |
\includegraphics[width = \linewidth]{./figures/dualLinear.pdf} |
502 |
\caption{Example least squares regressions of the configuration energy |
503 |
differences for SPC/E water systems. The upper plot shows a data set |
504 |
with a poor correlation coefficient ($R^2$), while the lower plot |
505 |
shows a data set with a good correlation coefficient.} |
506 |
\label{fig:linearFit} |
507 |
\end{figure} |
508 |
|
509 |
Each of the seven system types (detailed in section \ref{sec:RepSims}) |
510 |
were represented using 500 independent configurations. Thus, each of |
511 |
the alternative (non-Ewald) electrostatic summation methods was |
512 |
evaluated using an accumulated 873,250 configurational energy |
513 |
differences. |
514 |
|
515 |
Results and discussion for the individual analysis of each of the |
516 |
system types appear in sections \ref{sec:IndividualResults}, while the |
517 |
cumulative results over all the investigated systems appear below in |
518 |
sections \ref{sec:EnergyResults}. |
519 |
|
520 |
\subsection{Molecular Dynamics and the Force and Torque |
521 |
Vectors}\label{sec:MDMethods} We evaluated the pairwise methods |
522 |
(outlined in section \ref{sec:ESMethods}) for use in MD simulations by |
523 |
comparing the force and torque vectors with those obtained using the |
524 |
reference Ewald summation ({\sc spme}). Both the magnitude and the |
525 |
direction of these vectors on each of the bodies in the system were |
526 |
analyzed. For the magnitude of these vectors, linear least squares |
527 |
regression analyses were performed as described previously for |
528 |
comparing $\Delta E$ values. Instead of a single energy difference |
529 |
between two system configurations, we compared the magnitudes of the |
530 |
forces (and torques) on each molecule in each configuration. For a |
531 |
system of 1000 water molecules and 40 ions, there are 1040 force |
532 |
vectors and 1000 torque vectors. With 500 configurations, this |
533 |
results in 520,000 force and 500,000 torque vector comparisons. |
534 |
Additionally, data from seven different system types was aggregated |
535 |
before the comparison was made. |
536 |
|
537 |
The {\it directionality} of the force and torque vectors was |
538 |
investigated through measurement of the angle ($\theta$) formed |
539 |
between those computed from the particular method and those from {\sc spme}, |
540 |
\begin{equation} |
541 |
\theta_f = \cos^{-1} \left(\hat{F}_\textrm{SPME} |
542 |
\cdot \hat{F}_\textrm{M}\right), |
543 |
\end{equation} |
544 |
where $\hat{F}_\textrm{M}$ is the unit vector pointing along the force |
545 |
vector computed using method M. Each of these $\theta$ values was |
546 |
accumulated in a distribution function and weighted by the area on the |
547 |
unit sphere. Since this distribution is a measure of angular error |
548 |
between two different electrostatic summation methods, there is no |
549 |
{\it a priori} reason for the profile to adhere to any specific |
550 |
shape. Thus, gaussian fits were used to measure the width of the |
551 |
resulting distributions. The variance ($\sigma^2$) was extracted from |
552 |
each of these fits and was used to compare distribution widths. |
553 |
Values of $\sigma^2$ near zero indicate vector directions |
554 |
indistinguishable from those calculated when using the reference |
555 |
method ({\sc spme}). |
556 |
|
557 |
\subsection{Short-time Dynamics} |
558 |
|
559 |
The effects of the alternative electrostatic summation methods on the |
560 |
short-time dynamics of charged systems were evaluated by considering a |
561 |
NaCl crystal at a temperature of 1000 K. A subset of the best |
562 |
performing pairwise methods was used in this comparison. The NaCl |
563 |
crystal was chosen to avoid possible complications from the treatment |
564 |
of orientational motion in molecular systems. All systems were |
565 |
started with the same initial positions and velocities. Simulations |
566 |
were performed under the microcanonical ensemble, and velocity |
567 |
autocorrelation functions (Eq. \ref{eq:vCorr}) were computed for each |
568 |
of the trajectories, |
569 |
\begin{equation} |
570 |
C_v(t) = \frac{\langle v(0)\cdot v(t)\rangle}{\langle v^2\rangle}. |
571 |
\label{eq:vCorr} |
572 |
\end{equation} |
573 |
Velocity autocorrelation functions require detailed short time data, |
574 |
thus velocity information was saved every 2fs over 10ps |
575 |
trajectories. Because the NaCl crystal is composed of two different |
576 |
atom types, the average of the two resulting velocity autocorrelation |
577 |
functions was used for comparisons. |
578 |
|
579 |
\subsection{Long-Time and Collective Motion}\label{sec:LongTimeMethods} |
580 |
|
581 |
The effects of the same subset of alternative electrostatic methods on |
582 |
the {\it long-time} dynamics of charged systems were evaluated using |
583 |
the same model system (NaCl crystals at 1000K). The power spectrum |
584 |
($I(\omega)$) was obtained via Fourier transform of the velocity |
585 |
autocorrelation function, |
586 |
\begin{equation} I(\omega) = |
587 |
\frac{1}{2\pi}\int^{\infty}_{-\infty}C_v(t)e^{-i\omega t}dt, |
588 |
\label{eq:powerSpec} |
589 |
\end{equation} |
590 |
where the frequency, $\omega=0,\ 1,\ ...,\ N-1$. Again, because the |
591 |
NaCl crystal is composed of two different atom types, the average of |
592 |
the two resulting power spectra was used for comparisons. Simulations |
593 |
were performed under the microcanonical ensemble, and velocity |
594 |
information was saved every 5fs over 100ps trajectories. |
595 |
|
596 |
\subsection{Representative Simulations}\label{sec:RepSims} |
597 |
A variety of representative molecular simulations were analyzed to |
598 |
determine the relative effectiveness of the pairwise summation |
599 |
techniques in reproducing the energetics and dynamics exhibited by |
600 |
{\sc spme}. We wanted to span the space of typical molecular |
601 |
simulations (i.e. from liquids of neutral molecules to ionic |
602 |
crystals), so the systems studied were: |
603 |
|
604 |
\begin{enumerate}[itemsep=0pt] |
605 |
\item liquid water (SPC/E),\cite{Berendsen87} |
606 |
\item crystalline water (Ice I$_\textrm{c}$ crystals of SPC/E), |
607 |
\item NaCl crystals, |
608 |
\item NaCl melts, |
609 |
\item a low ionic strength solution of NaCl in water (0.11 M), |
610 |
\item a high ionic strength solution of NaCl in water (1.1 M), and |
611 |
\item a 6\AA\ radius sphere of Argon in water. |
612 |
\end{enumerate} |
613 |
|
614 |
By utilizing the pairwise techniques (outlined in section |
615 |
\ref{sec:ESMethods}) in systems composed entirely of neutral groups, |
616 |
charged particles, and mixtures of the two, we hope to discern under |
617 |
which conditions it will be possible to use one of the alternative |
618 |
summation methodologies instead of the Ewald sum. |
619 |
|
620 |
For the solid and liquid water configurations, configurations were |
621 |
taken at regular intervals from high temperature trajectories of 1000 |
622 |
SPC/E water molecules. Each configuration was equilibrated |
623 |
independently at a lower temperature (300K for the liquid, 200K for |
624 |
the crystal). The solid and liquid NaCl systems consisted of 500 |
625 |
$\textrm{Na}^{+}$ and 500 $\textrm{Cl}^{-}$ ions. Configurations for |
626 |
these systems were selected and equilibrated in the same manner as the |
627 |
water systems. In order to introduce measurable fluctuations in the |
628 |
configuration energy differences, the crystalline simulations were |
629 |
equilibrated at 1000K, near the $T_\textrm{m}$ for NaCl. The liquid |
630 |
NaCl configurations needed to represent a fully disordered array of |
631 |
point charges, so the high temperature of 7000K was selected for |
632 |
equilibration. The ionic solutions were made by solvating 4 (or 40) |
633 |
ions in a periodic box containing 1000 SPC/E water molecules. Ion and |
634 |
water positions were then randomly swapped, and the resulting |
635 |
configurations were again equilibrated individually. Finally, for the |
636 |
Argon / Water ``charge void'' systems, the identities of all the SPC/E |
637 |
waters within 6\AA\ of the center of the equilibrated water |
638 |
configurations were converted to argon. |
639 |
|
640 |
These procedures guaranteed us a set of representative configurations |
641 |
from chemically-relevant systems sampled from appropriate |
642 |
ensembles. Force field parameters for the ions and Argon were taken |
643 |
from the force field utilized by {\sc oopse}.\cite{Meineke05} |
644 |
|
645 |
\subsection{Comparison of Summation Methods}\label{sec:ESMethods} |
646 |
We compared the following alternative summation methods with results |
647 |
from the reference method ({\sc spme}): |
648 |
|
649 |
\begin{enumerate}[itemsep=0pt] |
650 |
\item {\sc sp} with damping parameters ($\alpha$) of 0.0, 0.1, 0.2, |
651 |
and 0.3\AA$^{-1}$, |
652 |
\item {\sc sf} with damping parameters ($\alpha$) of 0.0, 0.1, 0.2, |
653 |
and 0.3\AA$^{-1}$, |
654 |
\item reaction field with an infinite dielectric constant, and |
655 |
\item an unmodified cutoff. |
656 |
\end{enumerate} |
657 |
|
658 |
Group-based cutoffs with a fifth-order polynomial switching function |
659 |
were utilized for the reaction field simulations. Additionally, we |
660 |
investigated the use of these cutoffs with the {\sc sp}, {\sc sf}, and pure |
661 |
cutoff. The {\sc spme} electrostatics were performed using the {\sc tinker} |
662 |
implementation of {\sc spme},\cite{Ponder87} while all other calculations |
663 |
were performed using the {\sc oopse} molecular mechanics |
664 |
package.\cite{Meineke05} All other portions of the energy calculation |
665 |
(i.e. Lennard-Jones interactions) were handled in exactly the same |
666 |
manner across all systems and configurations. |
667 |
|
668 |
The alternative methods were also evaluated with three different |
669 |
cutoff radii (9, 12, and 15\AA). As noted previously, the |
670 |
convergence parameter ($\alpha$) plays a role in the balance of the |
671 |
real-space and reciprocal-space portions of the Ewald calculation. |
672 |
Typical molecular mechanics packages set this to a value dependent on |
673 |
the cutoff radius and a tolerance (typically less than $1 \times |
674 |
10^{-4}$ kcal/mol). Smaller tolerances are typically associated with |
675 |
increasing accuracy at the expense of computational time spent on the |
676 |
reciprocal-space portion of the summation.\cite{Perram88,Essmann95} |
677 |
The default {\sc tinker} tolerance of $1 \times 10^{-8}$ kcal/mol was used |
678 |
in all {\sc spme} calculations, resulting in Ewald coefficients of 0.4200, |
679 |
0.3119, and 0.2476\AA$^{-1}$ for cutoff radii of 9, 12, and 15\AA\ |
680 |
respectively. |
681 |
|
682 |
\section{Configuration Energy Difference Results}\label{sec:EnergyResults} |
683 |
In order to evaluate the performance of the pairwise electrostatic |
684 |
summation methods for Monte Carlo (MC) simulations, the energy |
685 |
differences between configurations were compared to the values |
686 |
obtained when using {\sc spme}. The results for the combined |
687 |
regression analysis of all of the systems are shown in figure |
688 |
\ref{fig:delE}. |
689 |
|
690 |
\begin{figure} |
691 |
\centering |
692 |
\includegraphics[width=4.75in]{./figures/delEplot.pdf} |
693 |
\caption{Statistical analysis of the quality of configurational energy |
694 |
differences for a given electrostatic method compared with the |
695 |
reference Ewald sum. Results with a value equal to 1 (dashed line) |
696 |
indicate $\Delta E$ values indistinguishable from those obtained using |
697 |
{\sc spme}. Different values of the cutoff radius are indicated with |
698 |
different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = |
699 |
inverted triangles).} |
700 |
\label{fig:delE} |
701 |
\end{figure} |
702 |
|
703 |
The most striking feature of this plot is how well the Shifted Force |
704 |
({\sc sf}) and Shifted Potential ({\sc sp}) methods capture the energy |
705 |
differences. For the undamped {\sc sf} method, and the |
706 |
moderately-damped {\sc sp} methods, the results are nearly |
707 |
indistinguishable from the Ewald results. The other common methods do |
708 |
significantly less well. |
709 |
|
710 |
The unmodified cutoff method is essentially unusable. This is not |
711 |
surprising since hard cutoffs give large energy fluctuations as atoms |
712 |
or molecules move in and out of the cutoff |
713 |
radius.\cite{Rahman71,Adams79} These fluctuations can be alleviated to |
714 |
some degree by using group based cutoffs with a switching |
715 |
function.\cite{Adams79,Steinbach94,Leach01} However, we do not see |
716 |
significant improvement using the group-switched cutoff because the |
717 |
salt and salt solution systems contain non-neutral groups. Section |
718 |
\ref{sec:IndividualResults} includes results for systems comprised entirely |
719 |
of neutral groups. |
720 |
|
721 |
For the {\sc sp} method, inclusion of electrostatic damping improves |
722 |
the agreement with Ewald, and using an $\alpha$ of 0.2\AA $^{-1}$ |
723 |
shows an excellent correlation and quality of fit with the {\sc spme} |
724 |
results, particularly with a cutoff radius greater than 12 |
725 |
\AA . Use of a larger damping parameter is more helpful for the |
726 |
shortest cutoff shown, but it has a detrimental effect on simulations |
727 |
with larger cutoffs. |
728 |
|
729 |
In the {\sc sf} sets, increasing damping results in progressively {\it |
730 |
worse} correlation with Ewald. Overall, the undamped case is the best |
731 |
performing set, as the correlation and quality of fits are |
732 |
consistently superior regardless of the cutoff distance. The undamped |
733 |
case is also less computationally demanding (because no evaluation of |
734 |
the complementary error function is required). |
735 |
|
736 |
The reaction field results illustrates some of that method's |
737 |
limitations, primarily that it was developed for use in homogeneous |
738 |
systems; although it does provide results that are an improvement over |
739 |
those from an unmodified cutoff. |
740 |
|
741 |
\section{Magnitude of the Force and Torque Vector Results}\label{sec:FTMagResults} |
742 |
|
743 |
Evaluation of pairwise methods for use in Molecular Dynamics |
744 |
simulations requires consideration of effects on the forces and |
745 |
torques. Figures \ref{fig:frcMag} and \ref{fig:trqMag} show the |
746 |
regression results for the force and torque vector magnitudes, |
747 |
respectively. The data in these figures was generated from an |
748 |
accumulation of the statistics from all of the system types. |
749 |
|
750 |
\begin{figure} |
751 |
\centering |
752 |
\includegraphics[width=4.75in]{./figures/frcMagplot.pdf} |
753 |
\caption{Statistical analysis of the quality of the force vector |
754 |
magnitudes for a given electrostatic method compared with the |
755 |
reference Ewald sum. Results with a value equal to 1 (dashed line) |
756 |
indicate force magnitude values indistinguishable from those obtained |
757 |
using {\sc spme}. Different values of the cutoff radius are indicated with |
758 |
different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = |
759 |
inverted triangles).} |
760 |
\label{fig:frcMag} |
761 |
\end{figure} |
762 |
|
763 |
Again, it is striking how well the Shifted Potential and Shifted Force |
764 |
methods are doing at reproducing the {\sc spme} forces. The undamped and |
765 |
weakly-damped {\sc sf} method gives the best agreement with Ewald. |
766 |
This is perhaps expected because this method explicitly incorporates a |
767 |
smooth transition in the forces at the cutoff radius as well as the |
768 |
neutralizing image charges. |
769 |
|
770 |
Figure \ref{fig:frcMag}, for the most part, parallels the results seen |
771 |
in the previous $\Delta E$ section. The unmodified cutoff results are |
772 |
poor, but using group based cutoffs and a switching function provides |
773 |
an improvement much more significant than what was seen with $\Delta |
774 |
E$. |
775 |
|
776 |
With moderate damping and a large enough cutoff radius, the {\sc sp} |
777 |
method is generating usable forces. Further increases in damping, |
778 |
while beneficial for simulations with a cutoff radius of 9\AA\ , is |
779 |
detrimental to simulations with larger cutoff radii. |
780 |
|
781 |
The reaction field results are surprisingly good, considering the poor |
782 |
quality of the fits for the $\Delta E$ results. There is still a |
783 |
considerable degree of scatter in the data, but the forces correlate |
784 |
well with the Ewald forces in general. We note that the reaction |
785 |
field calculations do not include the pure NaCl systems, so these |
786 |
results are partly biased towards conditions in which the method |
787 |
performs more favorably. |
788 |
|
789 |
\begin{figure} |
790 |
\centering |
791 |
\includegraphics[width=4.75in]{./figures/trqMagplot.pdf} |
792 |
\caption{Statistical analysis of the quality of the torque vector |
793 |
magnitudes for a given electrostatic method compared with the |
794 |
reference Ewald sum. Results with a value equal to 1 (dashed line) |
795 |
indicate torque magnitude values indistinguishable from those obtained |
796 |
using {\sc spme}. Different values of the cutoff radius are indicated with |
797 |
different symbols (9\AA\ = circles, 12\AA\ = squares, and 15\AA\ = |
798 |
inverted triangles).} |
799 |
\label{fig:trqMag} |
800 |
\end{figure} |
801 |
|
802 |
Molecular torques were only available from the systems which contained |
803 |
rigid molecules (i.e. the systems containing water). The data in |
804 |
fig. \ref{fig:trqMag} is taken from this smaller sampling pool. |
805 |
|
806 |
Torques appear to be much more sensitive to charges at a longer |
807 |
distance. The striking feature in comparing the new electrostatic |
808 |
methods with {\sc spme} is how much the agreement improves with increasing |
809 |
cutoff radius. Again, the weakly damped and undamped {\sc sf} method |
810 |
appears to be reproducing the {\sc spme} torques most accurately. |
811 |
|
812 |
Water molecules are dipolar, and the reaction field method reproduces |
813 |
the effect of the surrounding polarized medium on each of the |
814 |
molecular bodies. Therefore it is not surprising that reaction field |
815 |
performs best of all of the methods on molecular torques. |
816 |
|
817 |
\section{Directionality of the Force and Torque Vector Results}\label{sec:FTDirResults} |
818 |
|
819 |
It is clearly important that a new electrostatic method can reproduce |
820 |
the magnitudes of the force and torque vectors obtained via the Ewald |
821 |
sum. However, the {\it directionality} of these vectors will also be |
822 |
vital in calculating dynamical quantities accurately. Force and |
823 |
torque directionalities were investigated by measuring the angles |
824 |
formed between these vectors and the same vectors calculated using |
825 |
{\sc spme}. The results (Fig. \ref{fig:frcTrqAng}) are compared through the |
826 |
variance ($\sigma^2$) of the Gaussian fits of the angle error |
827 |
distributions of the combined set over all system types. |
828 |
|
829 |
\begin{figure} |
830 |
\centering |
831 |
\includegraphics[width=4.75in]{./figures/frcTrqAngplot.pdf} |
832 |
\caption{Statistical analysis of the width of the angular distribution |
833 |
that the force and torque vectors from a given electrostatic method |
834 |
make with their counterparts obtained using the reference Ewald sum. |
835 |
Results with a variance ($\sigma^2$) equal to zero (dashed line) |
836 |
indicate force and torque directions indistinguishable from those |
837 |
obtained using {\sc spme}. Different values of the cutoff radius are |
838 |
indicated with different symbols (9\AA\ = circles, 12\AA\ = squares, |
839 |
and 15\AA\ = inverted triangles).} |
840 |
\label{fig:frcTrqAng} |
841 |
\end{figure} |
842 |
|
843 |
Both the force and torque $\sigma^2$ results from the analysis of the |
844 |
total accumulated system data are tabulated in figure |
845 |
\ref{fig:frcTrqAng}. Here it is clear that the Shifted Potential ({\sc |
846 |
sp}) method would be essentially unusable for molecular dynamics |
847 |
unless the damping function is added. The Shifted Force ({\sc sf}) |
848 |
method, however, is generating force and torque vectors which are |
849 |
within a few degrees of the Ewald results even with weak (or no) |
850 |
damping. |
851 |
|
852 |
All of the sets (aside from the over-damped case) show the improvement |
853 |
afforded by choosing a larger cutoff radius. Increasing the cutoff |
854 |
from 9 to 12\AA\ typically results in a halving of the width of the |
855 |
distribution, with a similar improvement when going from 12 to 15 |
856 |
\AA . |
857 |
|
858 |
The undamped {\sc sf}, group-based cutoff, and reaction field methods |
859 |
all do equivalently well at capturing the direction of both the force |
860 |
and torque vectors. Using the electrostatic damping improves the |
861 |
angular behavior significantly for the {\sc sp} and moderately for the |
862 |
{\sc sf} methods. Over-damping is detrimental to both methods. Again |
863 |
it is important to recognize that the force vectors cover all |
864 |
particles in all seven systems, while torque vectors are only |
865 |
available for neutral molecular groups. Damping is more beneficial to |
866 |
charged bodies, and this observation is investigated further in |
867 |
section \ref{sec:IndividualResults}. |
868 |
|
869 |
Although not discussed previously, group based cutoffs can be applied |
870 |
to both the {\sc sp} and {\sc sf} methods. The group-based cutoffs |
871 |
will reintroduce small discontinuities at the cutoff radius, but the |
872 |
effects of these can be minimized by utilizing a switching function. |
873 |
Though there are no significant benefits or drawbacks observed in |
874 |
$\Delta E$ and the force and torque magnitudes when doing this, there |
875 |
is a measurable improvement in the directionality of the forces and |
876 |
torques. Table \ref{tab:groupAngle} shows the angular variances |
877 |
obtained both without (N) and with (Y) group based cutoffs and a |
878 |
switching function. Note that the $\alpha$ values have units of |
879 |
\AA$^{-1}$ and the variance values have units of degrees$^2$. The |
880 |
{\sc sp} (with an $\alpha$ of 0.2\AA$^{-1}$ or smaller) shows much |
881 |
narrower angular distributions when using group-based cutoffs. The |
882 |
{\sc sf} method likewise shows improvement in the undamped and lightly |
883 |
damped cases. |
884 |
|
885 |
\begin{table} |
886 |
\caption{STATISTICAL ANALYSIS OF THE ANGULAR DISTRIBUTIONS ($\sigma^2$) |
887 |
THAT THE FORCE ({\it upper}) AND TORQUE ({\it lower}) VECTORS FROM A |
888 |
GIVEN ELECTROSTATIC METHOD MAKE WITH THEIR COUNTERPARTS OBTAINED USING |
889 |
THE REFERENCE EWALD SUMMATION} |
890 |
|
891 |
\footnotesize |
892 |
\begin{center} |
893 |
\begin{tabular}{@{} ccrrrrrrrr @{}} |
894 |
\toprule |
895 |
\toprule |
896 |
& &\multicolumn{4}{c}{Shifted Potential} & \multicolumn{4}{c}{Shifted |
897 |
Force} \\ |
898 |
\cmidrule(lr){3-6} \cmidrule(l){7-10} $R_\textrm{c}$ & Groups & |
899 |
$\alpha = 0$ & $\alpha = 0.1$ & $\alpha = 0.2$ & $\alpha = 0.3$ & |
900 |
$\alpha = 0$ & $\alpha = 0.1$ & $\alpha = 0.2$ & $\alpha = 0.3$\\ |
901 |
|
902 |
\midrule |
903 |
|
904 |
9\AA & N & 29.545 & 12.003 & 5.489 & 0.610 & 2.323 & 2.321 & 0.429 & 0.603 \\ |
905 |
& \textbf{Y} & \textbf{2.486} & \textbf{2.160} & \textbf{0.667} & \textbf{0.608} & \textbf{1.768} & \textbf{1.766} & \textbf{0.676} & \textbf{0.609} \\ |
906 |
12\AA & N & 19.381 & 3.097 & 0.190 & 0.608 & 0.920 & 0.736 & 0.133 & 0.612 \\ |
907 |
& \textbf{Y} & \textbf{0.515} & \textbf{0.288} & \textbf{0.127} & \textbf{0.586} & \textbf{0.308} & \textbf{0.249} & \textbf{0.127} & \textbf{0.586} \\ |
908 |
15\AA & N & 12.700 & 1.196 & 0.123 & 0.601 & 0.339 & 0.160 & 0.123 & 0.601 \\ |
909 |
& \textbf{Y} & \textbf{0.228} & \textbf{0.099} & \textbf{0.121} & \textbf{0.598} & \textbf{0.144} & \textbf{0.090} & \textbf{0.121} & \textbf{0.598} \\ |
910 |
|
911 |
\midrule |
912 |
|
913 |
9\AA & N & 262.716 & 116.585 & 5.234 & 5.103 & 2.392 & 2.350 & 1.770 & 5.122 \\ |
914 |
& \textbf{Y} & \textbf{2.115} & \textbf{1.914} & \textbf{1.878} & \textbf{5.142} & \textbf{2.076} & \textbf{2.039} & \textbf{1.972} & \textbf{5.146} \\ |
915 |
12\AA & N & 129.576 & 25.560 & 1.369 & 5.080 & 0.913 & 0.790 & 1.362 & 5.124 \\ |
916 |
& \textbf{Y} & \textbf{0.810} & \textbf{0.685} & \textbf{1.352} & \textbf{5.082} & \textbf{0.765} & \textbf{0.714} & \textbf{1.360} & \textbf{5.082} \\ |
917 |
15\AA & N & 87.275 & 4.473 & 1.271 & 5.000 & 0.372 & 0.312 & 1.271 & 5.000 \\ |
918 |
& \textbf{Y} & \textbf{0.282} & \textbf{0.294} & \textbf{1.272} & \textbf{4.999} & \textbf{0.324} & \textbf{0.318} & \textbf{1.272} & \textbf{4.999} \\ |
919 |
|
920 |
\bottomrule |
921 |
\end{tabular} |
922 |
\end{center} |
923 |
\label{tab:groupAngle} |
924 |
\end{table} |
925 |
|
926 |
One additional trend in table \ref{tab:groupAngle} is that the |
927 |
$\sigma^2$ values for both {\sc sp} and {\sc sf} converge as $\alpha$ |
928 |
increases, something that is more obvious with group-based cutoffs. |
929 |
The complimentary error function inserted into the potential weakens |
930 |
the electrostatic interaction as the value of $\alpha$ is increased. |
931 |
However, at larger values of $\alpha$, it is possible to over-damp the |
932 |
electrostatic interaction and to remove it completely. Kast |
933 |
\textit{et al.} developed a method for choosing appropriate $\alpha$ |
934 |
values for these types of electrostatic summation methods by fitting |
935 |
to $g(r)$ data, and their methods indicate optimal values of 0.34, |
936 |
0.25, and 0.16\AA$^{-1}$ for cutoff values of 9, 12, and 15\AA\ |
937 |
respectively.\cite{Kast03} These appear to be reasonable choices to |
938 |
obtain proper MC behavior (Fig. \ref{fig:delE}); however, based on |
939 |
these findings, choices this high would introduce error in the |
940 |
molecular torques, particularly for the shorter cutoffs. Based on our |
941 |
observations, empirical damping up to 0.2\AA$^{-1}$ is beneficial, |
942 |
but damping may be unnecessary when using the {\sc sf} method. |
943 |
|
944 |
\section{Individual System Analysis Results}\label{sec:IndividualResults} |
945 |
|
946 |
The combined results of the previous sections show how the pairwise |
947 |
methods compare to the Ewald summation in the general sense over all |
948 |
of the system types. It is also useful to consider each of the |
949 |
studied systems in an individual fashion, so that we can identify |
950 |
conditions that are particularly difficult for a selected pairwise |
951 |
method to address. This allows us to further establish the limitations |
952 |
of these pairwise techniques. Below, the energy difference, force |
953 |
vector, and torque vector analyses are presented on an individual |
954 |
system basis. |
955 |
|
956 |
\subsection{SPC/E Water Results}\label{sec:WaterResults} |
957 |
|
958 |
The first system considered was liquid water at 300K using the SPC/E |
959 |
model of water.\cite{Berendsen87} The results for the energy gap |
960 |
comparisons and the force and torque vector magnitude comparisons are |
961 |
shown in table \ref{tab:spce}. The force and torque vector |
962 |
directionality results are displayed separately in table |
963 |
\ref{tab:spceAng}, where the effect of group-based cutoffs and |
964 |
switching functions on the {\sc sp} and {\sc sf} potentials are also |
965 |
investigated. In all of the individual results table, the method |
966 |
abbreviations are as follows: |
967 |
|
968 |
\begin{itemize}[itemsep=0pt] |
969 |
\item PC = Pure Cutoff, |
970 |
\item SP = Shifted Potential, |
971 |
\item SF = Shifted Force, |
972 |
\item GSC = Group Switched Cutoff, |
973 |
\item RF = Reaction Field (where $\varepsilon \approx\infty$), |
974 |
\item GSSP = Group Switched Shifted Potential, and |
975 |
\item GSSF = Group Switched Shifted Force. |
976 |
\end{itemize} |
977 |
|
978 |
\begin{table}[htbp] |
979 |
\centering |
980 |
\caption{REGRESSION RESULTS OF THE LIQUID WATER SYSTEM FOR THE |
981 |
$\Delta E$ VALUES ({\it upper}), FORCE VECTOR MAGNITUDES ({\it middle}) |
982 |
AND TORQUE VECTOR MAGNITUDES ({\it lower})} |
983 |
|
984 |
\footnotesize |
985 |
\begin{tabular}{@{} ccrrrrrr @{}} |
986 |
\toprule |
987 |
\toprule |
988 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
989 |
\cmidrule(lr){3-4} |
990 |
\cmidrule(lr){5-6} |
991 |
\cmidrule(l){7-8} |
992 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
993 |
\midrule |
994 |
PC & & 3.046 & 0.002 & -3.018 & 0.002 & 4.719 & 0.005 \\ |
995 |
SP & 0.0 & 1.035 & 0.218 & 0.908 & 0.313 & 1.037 & 0.470 \\ |
996 |
& 0.1 & 1.021 & 0.387 & 0.965 & 0.752 & 1.006 & 0.947 \\ |
997 |
& 0.2 & 0.997 & 0.962 & 1.001 & 0.994 & 0.994 & 0.996 \\ |
998 |
& 0.3 & 0.984 & 0.980 & 0.997 & 0.985 & 0.982 & 0.987 \\ |
999 |
SF & 0.0 & 0.977 & 0.974 & 0.996 & 0.992 & 0.991 & 0.997 \\ |
1000 |
& 0.1 & 0.983 & 0.974 & 1.001 & 0.994 & 0.996 & 0.998 \\ |
1001 |
& 0.2 & 0.992 & 0.989 & 1.001 & 0.995 & 0.994 & 0.996 \\ |
1002 |
& 0.3 & 0.984 & 0.980 & 0.996 & 0.985 & 0.982 & 0.987 \\ |
1003 |
GSC & & 0.918 & 0.862 & 0.852 & 0.756 & 0.801 & 0.700 \\ |
1004 |
RF & & 0.971 & 0.958 & 0.975 & 0.987 & 0.959 & 0.983 \\ |
1005 |
\midrule |
1006 |
PC & & -1.647 & 0.000 & -0.127 & 0.000 & -0.979 & 0.000 \\ |
1007 |
SP & 0.0 & 0.735 & 0.368 & 0.813 & 0.537 & 0.865 & 0.659 \\ |
1008 |
& 0.1 & 0.850 & 0.612 & 0.956 & 0.887 & 0.992 & 0.979 \\ |
1009 |
& 0.2 & 0.996 & 0.989 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1010 |
& 0.3 & 0.996 & 0.998 & 0.997 & 0.998 & 0.996 & 0.998 \\ |
1011 |
SF & 0.0 & 0.998 & 0.995 & 1.000 & 0.999 & 1.000 & 0.999 \\ |
1012 |
& 0.1 & 0.998 & 0.995 & 1.000 & 0.999 & 1.000 & 1.000 \\ |
1013 |
& 0.2 & 0.999 & 0.998 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1014 |
& 0.3 & 0.996 & 0.998 & 0.997 & 0.998 & 0.996 & 0.998 \\ |
1015 |
GSC & & 0.998 & 0.995 & 1.000 & 0.999 & 1.000 & 1.000 \\ |
1016 |
RF & & 0.999 & 0.995 & 1.000 & 0.999 & 1.000 & 1.000 \\ |
1017 |
\midrule |
1018 |
PC & & 2.387 & 0.000 & 0.183 & 0.000 & 1.282 & 0.000 \\ |
1019 |
SP & 0.0 & 0.847 & 0.543 & 0.904 & 0.694 & 0.935 & 0.786 \\ |
1020 |
& 0.1 & 0.922 & 0.749 & 0.980 & 0.934 & 0.996 & 0.988 \\ |
1021 |
& 0.2 & 0.987 & 0.985 & 0.989 & 0.992 & 0.990 & 0.993 \\ |
1022 |
& 0.3 & 0.965 & 0.973 & 0.967 & 0.975 & 0.967 & 0.976 \\ |
1023 |
SF & 0.0 & 0.978 & 0.990 & 0.988 & 0.997 & 0.993 & 0.999 \\ |
1024 |
& 0.1 & 0.983 & 0.991 & 0.993 & 0.997 & 0.997 & 0.999 \\ |
1025 |
& 0.2 & 0.986 & 0.989 & 0.989 & 0.992 & 0.990 & 0.993 \\ |
1026 |
& 0.3 & 0.965 & 0.973 & 0.967 & 0.975 & 0.967 & 0.976 \\ |
1027 |
GSC & & 0.995 & 0.981 & 0.999 & 0.991 & 1.001 & 0.994 \\ |
1028 |
RF & & 0.993 & 0.989 & 0.998 & 0.996 & 1.000 & 0.999 \\ |
1029 |
\bottomrule |
1030 |
\end{tabular} |
1031 |
\label{tab:spce} |
1032 |
\end{table} |
1033 |
|
1034 |
\begin{table}[htbp] |
1035 |
\centering |
1036 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR |
1037 |
DISTRIBUTIONS OF THE FORCE AND TORQUE VECTORS IN THE LIQUID WATER |
1038 |
SYSTEM} |
1039 |
|
1040 |
\footnotesize |
1041 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1042 |
\toprule |
1043 |
\toprule |
1044 |
& & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\ |
1045 |
\cmidrule(lr){3-5} |
1046 |
\cmidrule(l){6-8} |
1047 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA & 9\AA & 12\AA & 15\AA \\ |
1048 |
\midrule |
1049 |
PC & & 783.759 & 481.353 & 332.677 & 248.674 & 144.382 & 98.535 \\ |
1050 |
SP & 0.0 & 659.440 & 380.699 & 250.002 & 235.151 & 134.661 & 88.135 \\ |
1051 |
& 0.1 & 293.849 & 67.772 & 11.609 & 105.090 & 23.813 & 4.369 \\ |
1052 |
& 0.2 & 5.975 & 0.136 & 0.094 & 5.553 & 1.784 & 1.536 \\ |
1053 |
& 0.3 & 0.725 & 0.707 & 0.693 & 7.293 & 6.933 & 6.748 \\ |
1054 |
SF & 0.0 & 2.238 & 0.713 & 0.292 & 3.290 & 1.090 & 0.416 \\ |
1055 |
& 0.1 & 2.238 & 0.524 & 0.115 & 3.184 & 0.945 & 0.326 \\ |
1056 |
& 0.2 & 0.374 & 0.102 & 0.094 & 2.598 & 1.755 & 1.537 \\ |
1057 |
& 0.3 & 0.721 & 0.707 & 0.693 & 7.322 & 6.933 & 6.748 \\ |
1058 |
GSC & & 2.431 & 0.614 & 0.274 & 5.135 & 2.133 & 1.339 \\ |
1059 |
RF & & 2.091 & 0.403 & 0.113 & 3.583 & 1.071 & 0.399 \\ |
1060 |
\midrule |
1061 |
GSSP & 0.0 & 2.431 & 0.614 & 0.274 & 5.135 & 2.133 & 1.339 \\ |
1062 |
& 0.1 & 1.879 & 0.291 & 0.057 & 3.983 & 1.117 & 0.370 \\ |
1063 |
& 0.2 & 0.443 & 0.103 & 0.093 & 2.821 & 1.794 & 1.532 \\ |
1064 |
& 0.3 & 0.728 & 0.694 & 0.692 & 7.387 & 6.942 & 6.748 \\ |
1065 |
GSSF & 0.0 & 1.298 & 0.270 & 0.083 & 3.098 & 0.992 & 0.375 \\ |
1066 |
& 0.1 & 1.296 & 0.210 & 0.044 & 3.055 & 0.922 & 0.330 \\ |
1067 |
& 0.2 & 0.433 & 0.104 & 0.093 & 2.895 & 1.797 & 1.532 \\ |
1068 |
& 0.3 & 0.728 & 0.694 & 0.692 & 7.410 & 6.942 & 6.748 \\ |
1069 |
\bottomrule |
1070 |
\end{tabular} |
1071 |
\label{tab:spceAng} |
1072 |
\end{table} |
1073 |
|
1074 |
The water results parallel the combined results seen in sections |
1075 |
\ref{sec:EnergyResults} through \ref{sec:FTDirResults}. There is good |
1076 |
agreement with {\sc spme} in both energetic and dynamic behavior when |
1077 |
using the {\sc sf} method with and without damping. The {\sc sp} |
1078 |
method does well with an $\alpha$ around 0.2\AA$^{-1}$, particularly |
1079 |
with cutoff radii greater than 12\AA. Over-damping the electrostatics |
1080 |
reduces the agreement between both these methods and {\sc spme}. |
1081 |
|
1082 |
The pure cutoff ({\sc pc}) method performs poorly, again mirroring the |
1083 |
observations from the combined results. In contrast to these results, however, the use of a switching function and group |
1084 |
based cutoffs greatly improves the results for these neutral water |
1085 |
molecules. The group switched cutoff ({\sc gsc}) does not mimic the |
1086 |
energetics of {\sc spme} as well as the {\sc sp} (with moderate |
1087 |
damping) and {\sc sf} methods, but the dynamics are quite good. The |
1088 |
switching functions correct discontinuities in the potential and |
1089 |
forces, leading to these improved results. Such improvements with the |
1090 |
use of a switching function have been recognized in previous |
1091 |
studies,\cite{Andrea83,Steinbach94} and this proves to be a useful |
1092 |
tactic for stably incorporating local area electrostatic effects. |
1093 |
|
1094 |
The reaction field ({\sc rf}) method simply extends upon the results |
1095 |
observed in the {\sc gsc} case. Both methods are similar in form |
1096 |
(i.e. neutral groups, switching function), but {\sc rf} incorporates |
1097 |
an added effect from the external dielectric. This similarity |
1098 |
translates into the same good dynamic results and improved energetic |
1099 |
agreement with {\sc spme}. Though this agreement is not to the level |
1100 |
of the moderately damped {\sc sp} and {\sc sf} methods, these results |
1101 |
show how incorporating some implicit properties of the surroundings |
1102 |
(i.e. $\epsilon_\textrm{S}$) can improve the solvent depiction. |
1103 |
|
1104 |
As a final note for the liquid water system, use of group cutoffs and a |
1105 |
switching function leads to noticeable improvements in the {\sc sp} |
1106 |
and {\sc sf} methods, primarily in directionality of the force and |
1107 |
torque vectors (table \ref{tab:spceAng}). The {\sc sp} method shows |
1108 |
significant narrowing of the angle distribution when using little to |
1109 |
no damping and only modest improvement for the recommended conditions |
1110 |
($\alpha = 0.2$\AA$^{-1}$ and $R_\textrm{c}~\geqslant~12$\AA). The |
1111 |
{\sc sf} method shows modest narrowing across all damping and cutoff |
1112 |
ranges of interest. When over-damping these methods, group cutoffs and |
1113 |
the switching function do not improve the force and torque |
1114 |
directionalities. |
1115 |
|
1116 |
\subsection{SPC/E Ice I$_\textrm{c}$ Results}\label{sec:IceResults} |
1117 |
|
1118 |
In addition to the disordered molecular system above, the ordered |
1119 |
molecular system of ice I$_\textrm{c}$ was also considered. Ice |
1120 |
polymorph could have been used to fit this role; however, ice |
1121 |
I$_\textrm{c}$ was chosen because it can form an ideal periodic |
1122 |
lattice with the same number of water molecules used in the disordered |
1123 |
liquid state case. The results for the energy gap comparisons and the |
1124 |
force and torque vector magnitude comparisons are shown in table |
1125 |
\ref{tab:ice}. The force and torque vector directionality results are |
1126 |
displayed separately in table \ref{tab:iceAng}, where the effect of |
1127 |
group-based cutoffs and switching functions on the {\sc sp} and {\sc |
1128 |
sf} potentials are also displayed. |
1129 |
|
1130 |
\begin{table}[htbp] |
1131 |
\centering |
1132 |
\caption{REGRESSION RESULTS OF THE ICE I$_\textrm{c}$ SYSTEM FOR |
1133 |
$\Delta E$ VALUES ({\it upper}), FORCE VECTOR MAGNITUDES ({\it |
1134 |
middle}) AND TORQUE VECTOR MAGNITUDES ({\it lower})} |
1135 |
|
1136 |
\footnotesize |
1137 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1138 |
\toprule |
1139 |
\toprule |
1140 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1141 |
\cmidrule(lr){3-4} |
1142 |
\cmidrule(lr){5-6} |
1143 |
\cmidrule(l){7-8} |
1144 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1145 |
\midrule |
1146 |
PC & & 19.897 & 0.047 & -29.214 & 0.048 & -3.771 & 0.001 \\ |
1147 |
SP & 0.0 & -0.014 & 0.000 & 2.135 & 0.347 & 0.457 & 0.045 \\ |
1148 |
& 0.1 & 0.321 & 0.017 & 1.490 & 0.584 & 0.886 & 0.796 \\ |
1149 |
& 0.2 & 0.896 & 0.872 & 1.011 & 0.998 & 0.997 & 0.999 \\ |
1150 |
& 0.3 & 0.983 & 0.997 & 0.992 & 0.997 & 0.991 & 0.997 \\ |
1151 |
SF & 0.0 & 0.943 & 0.979 & 1.048 & 0.978 & 0.995 & 0.999 \\ |
1152 |
& 0.1 & 0.948 & 0.979 & 1.044 & 0.983 & 1.000 & 0.999 \\ |
1153 |
& 0.2 & 0.982 & 0.997 & 0.969 & 0.960 & 0.997 & 0.999 \\ |
1154 |
& 0.3 & 0.985 & 0.997 & 0.961 & 0.961 & 0.991 & 0.997 \\ |
1155 |
GSC & & 0.983 & 0.985 & 0.966 & 0.994 & 1.003 & 0.999 \\ |
1156 |
RF & & 0.924 & 0.944 & 0.990 & 0.996 & 0.991 & 0.998 \\ |
1157 |
\midrule |
1158 |
PC & & -4.375 & 0.000 & 6.781 & 0.000 & -3.369 & 0.000 \\ |
1159 |
SP & 0.0 & 0.515 & 0.164 & 0.856 & 0.426 & 0.743 & 0.478 \\ |
1160 |
& 0.1 & 0.696 & 0.405 & 0.977 & 0.817 & 0.974 & 0.964 \\ |
1161 |
& 0.2 & 0.981 & 0.980 & 1.001 & 1.000 & 1.000 & 1.000 \\ |
1162 |
& 0.3 & 0.996 & 0.998 & 0.997 & 0.999 & 0.997 & 0.999 \\ |
1163 |
SF & 0.0 & 0.991 & 0.995 & 1.003 & 0.998 & 0.999 & 1.000 \\ |
1164 |
& 0.1 & 0.992 & 0.995 & 1.003 & 0.998 & 1.000 & 1.000 \\ |
1165 |
& 0.2 & 0.998 & 0.998 & 0.981 & 0.962 & 1.000 & 1.000 \\ |
1166 |
& 0.3 & 0.996 & 0.998 & 0.976 & 0.957 & 0.997 & 0.999 \\ |
1167 |
GSC & & 0.997 & 0.996 & 0.998 & 0.999 & 1.000 & 1.000 \\ |
1168 |
RF & & 0.988 & 0.989 & 1.000 & 0.999 & 1.000 & 1.000 \\ |
1169 |
\midrule |
1170 |
PC & & -6.367 & 0.000 & -3.552 & 0.000 & -3.447 & 0.000 \\ |
1171 |
SP & 0.0 & 0.643 & 0.409 & 0.833 & 0.607 & 0.961 & 0.805 \\ |
1172 |
& 0.1 & 0.791 & 0.683 & 0.957 & 0.914 & 1.000 & 0.989 \\ |
1173 |
& 0.2 & 0.974 & 0.991 & 0.993 & 0.998 & 0.993 & 0.998 \\ |
1174 |
& 0.3 & 0.976 & 0.992 & 0.977 & 0.992 & 0.977 & 0.992 \\ |
1175 |
SF & 0.0 & 0.979 & 0.997 & 0.992 & 0.999 & 0.994 & 1.000 \\ |
1176 |
& 0.1 & 0.984 & 0.997 & 0.996 & 0.999 & 0.998 & 1.000 \\ |
1177 |
& 0.2 & 0.991 & 0.997 & 0.974 & 0.958 & 0.993 & 0.998 \\ |
1178 |
& 0.3 & 0.977 & 0.992 & 0.956 & 0.948 & 0.977 & 0.992 \\ |
1179 |
GSC & & 0.999 & 0.997 & 0.996 & 0.999 & 1.002 & 1.000 \\ |
1180 |
RF & & 0.994 & 0.997 & 0.997 & 0.999 & 1.000 & 1.000 \\ |
1181 |
\bottomrule |
1182 |
\end{tabular} |
1183 |
\label{tab:ice} |
1184 |
\end{table} |
1185 |
|
1186 |
\begin{table}[htbp] |
1187 |
\centering |
1188 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR DISTRIBUTIONS |
1189 |
OF THE FORCE AND TORQUE VECTORS IN THE ICE I$_\textrm{c}$ SYSTEM} |
1190 |
|
1191 |
\footnotesize |
1192 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1193 |
\toprule |
1194 |
\toprule |
1195 |
& & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque |
1196 |
$\sigma^2$} \\ |
1197 |
\cmidrule(lr){3-5} |
1198 |
\cmidrule(l){6-8} |
1199 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA & 9\AA & 12\AA & 15\AA \\ |
1200 |
\midrule |
1201 |
PC & & 2128.921 & 603.197 & 715.579 & 329.056 & 221.397 & 81.042 \\ |
1202 |
SP & 0.0 & 1429.341 & 470.320 & 447.557 & 301.678 & 197.437 & 73.840 \\ |
1203 |
& 0.1 & 590.008 & 107.510 & 18.883 & 118.201 & 32.472 & 3.599 \\ |
1204 |
& 0.2 & 10.057 & 0.105 & 0.038 & 2.875 & 0.572 & 0.518 \\ |
1205 |
& 0.3 & 0.245 & 0.260 & 0.262 & 2.365 & 2.396 & 2.327 \\ |
1206 |
SF & 0.0 & 1.745 & 1.161 & 0.212 & 1.135 & 0.426 & 0.155 \\ |
1207 |
& 0.1 & 1.721 & 0.868 & 0.082 & 1.118 & 0.358 & 0.118 \\ |
1208 |
& 0.2 & 0.201 & 0.040 & 0.038 & 0.786 & 0.555 & 0.518 \\ |
1209 |
& 0.3 & 0.241 & 0.260 & 0.262 & 2.368 & 2.400 & 2.327 \\ |
1210 |
GSC & & 1.483 & 0.261 & 0.099 & 0.926 & 0.295 & 0.095 \\ |
1211 |
RF & & 2.887 & 0.217 & 0.107 & 1.006 & 0.281 & 0.085 \\ |
1212 |
\midrule |
1213 |
GSSP & 0.0 & 1.483 & 0.261 & 0.099 & 0.926 & 0.295 & 0.095 \\ |
1214 |
& 0.1 & 1.341 & 0.123 & 0.037 & 0.835 & 0.234 & 0.085 \\ |
1215 |
& 0.2 & 0.558 & 0.040 & 0.037 & 0.823 & 0.557 & 0.519 \\ |
1216 |
& 0.3 & 0.250 & 0.251 & 0.259 & 2.387 & 2.395 & 2.328 \\ |
1217 |
GSSF & 0.0 & 2.124 & 0.132 & 0.069 & 0.919 & 0.263 & 0.099 \\ |
1218 |
& 0.1 & 2.165 & 0.101 & 0.035 & 0.895 & 0.244 & 0.096 \\ |
1219 |
& 0.2 & 0.706 & 0.040 & 0.037 & 0.870 & 0.559 & 0.519 \\ |
1220 |
& 0.3 & 0.251 & 0.251 & 0.259 & 2.387 & 2.395 & 2.328 \\ |
1221 |
\bottomrule |
1222 |
\end{tabular} |
1223 |
\label{tab:iceAng} |
1224 |
\end{table} |
1225 |
|
1226 |
Highly ordered systems are a difficult test for the pairwise methods |
1227 |
in that they lack the implicit periodicity of the Ewald summation. As |
1228 |
expected, the energy gap agreement with {\sc spme} is reduced for the |
1229 |
{\sc sp} and {\sc sf} methods with parameters that were ideal for the |
1230 |
disordered liquid system. Moving to higher $R_\textrm{c}$ helps |
1231 |
improve the agreement, though at an increase in computational cost. |
1232 |
The dynamics of this crystalline system (both in magnitude and |
1233 |
direction) are little affected. Both methods still reproduce the Ewald |
1234 |
behavior with the same parameter recommendations from the previous |
1235 |
section. |
1236 |
|
1237 |
It is also worth noting that {\sc rf} exhibits improved energy gap |
1238 |
results over the liquid water system. One possible explanation is |
1239 |
that the ice I$_\textrm{c}$ crystal is ordered such that the net |
1240 |
dipole moment of the crystal is zero. With $\epsilon_\textrm{S} = |
1241 |
\infty$, the reaction field incorporates this structural organization |
1242 |
by actively enforcing a zeroed dipole moment within each cutoff |
1243 |
sphere. |
1244 |
|
1245 |
\subsection{NaCl Melt Results}\label{sec:SaltMeltResults} |
1246 |
|
1247 |
A high temperature NaCl melt was tested to gauge the accuracy of the |
1248 |
pairwise summation methods in a disordered system of charges. The |
1249 |
results for the energy gap comparisons and the force vector magnitude |
1250 |
comparisons are shown in table \ref{tab:melt}. The force vector |
1251 |
directionality results are displayed separately in table |
1252 |
\ref{tab:meltAng}. |
1253 |
|
1254 |
\begin{table}[htbp] |
1255 |
\centering |
1256 |
\caption{REGRESSION RESULTS OF THE MOLTEN SODIUM CHLORIDE SYSTEM FOR |
1257 |
$\Delta E$ VALUES ({\it upper}) AND FORCE VECTOR MAGNITUDES ({\it |
1258 |
lower})} |
1259 |
|
1260 |
\footnotesize |
1261 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1262 |
\toprule |
1263 |
\toprule |
1264 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1265 |
\cmidrule(lr){3-4} |
1266 |
\cmidrule(lr){5-6} |
1267 |
\cmidrule(l){7-8} |
1268 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1269 |
\midrule |
1270 |
PC & & -0.008 & 0.000 & -0.049 & 0.005 & -0.136 & 0.020 \\ |
1271 |
SP & 0.0 & 0.928 & 0.996 & 0.931 & 0.998 & 0.950 & 0.999 \\ |
1272 |
& 0.1 & 0.977 & 0.998 & 0.998 & 1.000 & 0.997 & 1.000 \\ |
1273 |
& 0.2 & 0.960 & 1.000 & 0.813 & 0.996 & 0.811 & 0.954 \\ |
1274 |
& 0.3 & 0.671 & 0.994 & 0.439 & 0.929 & 0.535 & 0.831 \\ |
1275 |
SF & 0.0 & 0.996 & 1.000 & 0.995 & 1.000 & 0.997 & 1.000 \\ |
1276 |
& 0.1 & 1.021 & 1.000 & 1.024 & 1.000 & 1.007 & 1.000 \\ |
1277 |
& 0.2 & 0.966 & 1.000 & 0.813 & 0.996 & 0.811 & 0.954 \\ |
1278 |
& 0.3 & 0.671 & 0.994 & 0.439 & 0.929 & 0.535 & 0.831 \\ |
1279 |
\midrule |
1280 |
PC & & 1.103 & 0.000 & 0.989 & 0.000 & 0.802 & 0.000 \\ |
1281 |
SP & 0.0 & 0.973 & 0.981 & 0.975 & 0.988 & 0.979 & 0.992 \\ |
1282 |
& 0.1 & 0.987 & 0.992 & 0.993 & 0.998 & 0.997 & 0.999 \\ |
1283 |
& 0.2 & 0.993 & 0.996 & 0.985 & 0.988 & 0.986 & 0.981 \\ |
1284 |
& 0.3 & 0.956 & 0.956 & 0.940 & 0.912 & 0.948 & 0.929 \\ |
1285 |
SF & 0.0 & 0.996 & 0.997 & 0.997 & 0.999 & 0.998 & 1.000 \\ |
1286 |
& 0.1 & 1.000 & 0.997 & 1.001 & 0.999 & 1.000 & 1.000 \\ |
1287 |
& 0.2 & 0.994 & 0.996 & 0.985 & 0.988 & 0.986 & 0.981 \\ |
1288 |
& 0.3 & 0.956 & 0.956 & 0.940 & 0.912 & 0.948 & 0.929 \\ |
1289 |
\bottomrule |
1290 |
\end{tabular} |
1291 |
\label{tab:melt} |
1292 |
\end{table} |
1293 |
|
1294 |
\begin{table}[htbp] |
1295 |
\centering |
1296 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR DISTRIBUTIONS |
1297 |
OF THE FORCE VECTORS IN THE MOLTEN SODIUM CHLORIDE SYSTEM} |
1298 |
|
1299 |
\footnotesize |
1300 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1301 |
\toprule |
1302 |
\toprule |
1303 |
& & \multicolumn{3}{c}{Force $\sigma^2$} \\ |
1304 |
\cmidrule(lr){3-5} |
1305 |
\cmidrule(l){6-8} |
1306 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA \\ |
1307 |
\midrule |
1308 |
PC & & 13.294 & 8.035 & 5.366 \\ |
1309 |
SP & 0.0 & 13.316 & 8.037 & 5.385 \\ |
1310 |
& 0.1 & 5.705 & 1.391 & 0.360 \\ |
1311 |
& 0.2 & 2.415 & 7.534 & 13.927 \\ |
1312 |
& 0.3 & 23.769 & 67.306 & 57.252 \\ |
1313 |
SF & 0.0 & 1.693 & 0.603 & 0.256 \\ |
1314 |
& 0.1 & 1.687 & 0.653 & 0.272 \\ |
1315 |
& 0.2 & 2.598 & 7.523 & 13.930 \\ |
1316 |
& 0.3 & 23.734 & 67.305 & 57.252 \\ |
1317 |
\bottomrule |
1318 |
\end{tabular} |
1319 |
\label{tab:meltAng} |
1320 |
\end{table} |
1321 |
|
1322 |
The molten NaCl system shows more sensitivity to the electrostatic |
1323 |
damping than the water systems. The most noticeable point is that the |
1324 |
undamped {\sc sf} method does very well at replicating the {\sc spme} |
1325 |
configurational energy differences and forces. Light damping appears |
1326 |
to minimally improve the dynamics, but this comes with a deterioration |
1327 |
of the energy gap results. In contrast, this light damping improves |
1328 |
the {\sc sp} energy gaps and forces. Moderate and heavy electrostatic |
1329 |
damping reduce the agreement with {\sc spme} for both methods. From |
1330 |
these observations, the undamped {\sc sf} method is the best choice |
1331 |
for disordered systems of charges. |
1332 |
|
1333 |
\subsection{NaCl Crystal Results}\label{sec:SaltCrystalResults} |
1334 |
|
1335 |
Similar to the use of ice I$_\textrm{c}$ to investigate the role of |
1336 |
order in molecular systems on the effectiveness of the pairwise |
1337 |
methods, the 1000K NaCl crystal system was used to investigate the |
1338 |
accuracy of the pairwise summation methods in an ordered system of |
1339 |
charged particles. The results for the energy gap comparisons and the |
1340 |
force vector magnitude comparisons are shown in table \ref{tab:salt}. |
1341 |
The force vector directionality results are displayed separately in |
1342 |
table \ref{tab:saltAng}. |
1343 |
|
1344 |
\begin{table}[htbp] |
1345 |
\centering |
1346 |
\caption{REGRESSION RESULTS OF THE CRYSTALLINE SODIUM CHLORIDE |
1347 |
SYSTEM FOR $\Delta E$ VALUES ({\it upper}) AND FORCE VECTOR MAGNITUDES |
1348 |
({\it lower})} |
1349 |
|
1350 |
\footnotesize |
1351 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1352 |
\toprule |
1353 |
\toprule |
1354 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1355 |
\cmidrule(lr){3-4} |
1356 |
\cmidrule(lr){5-6} |
1357 |
\cmidrule(l){7-8} |
1358 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1359 |
\midrule |
1360 |
PC & & -20.241 & 0.228 & -20.248 & 0.229 & -20.239 & 0.228 \\ |
1361 |
SP & 0.0 & 1.039 & 0.733 & 2.037 & 0.565 & 1.225 & 0.743 \\ |
1362 |
& 0.1 & 1.049 & 0.865 & 1.424 & 0.784 & 1.029 & 0.980 \\ |
1363 |
& 0.2 & 0.982 & 0.976 & 0.969 & 0.980 & 0.960 & 0.980 \\ |
1364 |
& 0.3 & 0.873 & 0.944 & 0.872 & 0.945 & 0.872 & 0.945 \\ |
1365 |
SF & 0.0 & 1.041 & 0.967 & 0.994 & 0.989 & 0.957 & 0.993 \\ |
1366 |
& 0.1 & 1.050 & 0.968 & 0.996 & 0.991 & 0.972 & 0.995 \\ |
1367 |
& 0.2 & 0.982 & 0.975 & 0.959 & 0.980 & 0.960 & 0.980 \\ |
1368 |
& 0.3 & 0.873 & 0.944 & 0.872 & 0.945 & 0.872 & 0.944 \\ |
1369 |
\midrule |
1370 |
PC & & 0.795 & 0.000 & 0.792 & 0.000 & 0.793 & 0.000 \\ |
1371 |
SP & 0.0 & 0.916 & 0.829 & 1.086 & 0.791 & 1.010 & 0.936 \\ |
1372 |
& 0.1 & 0.958 & 0.917 & 1.049 & 0.943 & 1.001 & 0.995 \\ |
1373 |
& 0.2 & 0.981 & 0.981 & 0.982 & 0.984 & 0.981 & 0.984 \\ |
1374 |
& 0.3 & 0.950 & 0.952 & 0.950 & 0.953 & 0.950 & 0.953 \\ |
1375 |
SF & 0.0 & 1.002 & 0.983 & 0.997 & 0.994 & 0.991 & 0.997 \\ |
1376 |
& 0.1 & 1.003 & 0.984 & 0.996 & 0.995 & 0.993 & 0.997 \\ |
1377 |
& 0.2 & 0.983 & 0.980 & 0.981 & 0.984 & 0.981 & 0.984 \\ |
1378 |
& 0.3 & 0.950 & 0.952 & 0.950 & 0.953 & 0.950 & 0.953 \\ |
1379 |
\bottomrule |
1380 |
\end{tabular} |
1381 |
\label{tab:salt} |
1382 |
\end{table} |
1383 |
|
1384 |
\begin{table}[htbp] |
1385 |
\centering |
1386 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR |
1387 |
DISTRIBUTIONS OF THE FORCE VECTORS IN THE CRYSTALLINE SODIUM CHLORIDE |
1388 |
SYSTEM} |
1389 |
|
1390 |
\footnotesize |
1391 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1392 |
\toprule |
1393 |
\toprule |
1394 |
& & \multicolumn{3}{c}{Force $\sigma^2$} \\ |
1395 |
\cmidrule(lr){3-5} |
1396 |
\cmidrule(l){6-8} |
1397 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA \\ |
1398 |
\midrule |
1399 |
PC & & 111.945 & 111.824 & 111.866 \\ |
1400 |
SP & 0.0 & 112.414 & 152.215 & 38.087 \\ |
1401 |
& 0.1 & 52.361 & 42.574 & 2.819 \\ |
1402 |
& 0.2 & 10.847 & 9.709 & 9.686 \\ |
1403 |
& 0.3 & 31.128 & 31.104 & 31.029 \\ |
1404 |
SF & 0.0 & 10.025 & 3.555 & 1.648 \\ |
1405 |
& 0.1 & 9.462 & 3.303 & 1.721 \\ |
1406 |
& 0.2 & 11.454 & 9.813 & 9.701 \\ |
1407 |
& 0.3 & 31.120 & 31.105 & 31.029 \\ |
1408 |
\bottomrule |
1409 |
\end{tabular} |
1410 |
\label{tab:saltAng} |
1411 |
\end{table} |
1412 |
|
1413 |
The crystalline NaCl system is the most challenging test case for the |
1414 |
pairwise summation methods, as evidenced by the results in tables |
1415 |
\ref{tab:salt} and \ref{tab:saltAng}. The undamped and weakly damped |
1416 |
{\sc sf} methods seem to be the best choices. These methods match well |
1417 |
with {\sc spme} across the energy gap, force magnitude, and force |
1418 |
directionality tests. The {\sc sp} method struggles in all cases, |
1419 |
with the exception of good dynamics reproduction when using weak |
1420 |
electrostatic damping with a large cutoff radius. |
1421 |
|
1422 |
The moderate electrostatic damping case is not as good as we would |
1423 |
expect given the long-time dynamics results observed for this system |
1424 |
(see section \ref{sec:LongTimeDynamics}). Since the data tabulated in |
1425 |
tables \ref{tab:salt} and \ref{tab:saltAng} are a test of |
1426 |
instantaneous dynamics, this indicates that good long-time dynamics |
1427 |
comes in part at the expense of short-time dynamics. |
1428 |
|
1429 |
\subsection{0.11M NaCl Solution Results} |
1430 |
|
1431 |
In an effort to bridge the charged atomic and neutral molecular |
1432 |
systems, Na$^+$ and Cl$^-$ ion charge defects were incorporated into |
1433 |
the liquid water system. This low ionic strength system consists of 4 |
1434 |
ions in the 1000 SPC/E water solvent ($\approx$0.11 M). The results |
1435 |
for the energy gap comparisons and the force and torque vector |
1436 |
magnitude comparisons are shown in table \ref{tab:solnWeak}. The |
1437 |
force and torque vector directionality results are displayed |
1438 |
separately in table \ref{tab:solnWeakAng}, where the effect of |
1439 |
group-based cutoffs and switching functions on the {\sc sp} and {\sc |
1440 |
sf} potentials are investigated. |
1441 |
|
1442 |
\begin{table}[htbp] |
1443 |
\centering |
1444 |
\caption{REGRESSION RESULTS OF THE WEAK SODIUM CHLORIDE SOLUTION |
1445 |
SYSTEM FOR $\Delta E$ VALUES ({\it upper}), FORCE VECTOR MAGNITUDES |
1446 |
({\it middle}) AND TORQUE VECTOR MAGNITUDES ({\it lower})} |
1447 |
|
1448 |
\footnotesize |
1449 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1450 |
\toprule |
1451 |
\toprule |
1452 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1453 |
\cmidrule(lr){3-4} |
1454 |
\cmidrule(lr){5-6} |
1455 |
\cmidrule(l){7-8} |
1456 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1457 |
\midrule |
1458 |
PC & & 0.247 & 0.000 & -1.103 & 0.001 & 5.480 & 0.015 \\ |
1459 |
SP & 0.0 & 0.935 & 0.388 & 0.984 & 0.541 & 1.010 & 0.685 \\ |
1460 |
& 0.1 & 0.951 & 0.603 & 0.993 & 0.875 & 1.001 & 0.979 \\ |
1461 |
& 0.2 & 0.969 & 0.968 & 0.996 & 0.997 & 0.994 & 0.997 \\ |
1462 |
& 0.3 & 0.955 & 0.966 & 0.984 & 0.992 & 0.978 & 0.991 \\ |
1463 |
SF & 0.0 & 0.963 & 0.971 & 0.989 & 0.996 & 0.991 & 0.998 \\ |
1464 |
& 0.1 & 0.970 & 0.971 & 0.995 & 0.997 & 0.997 & 0.999 \\ |
1465 |
& 0.2 & 0.972 & 0.975 & 0.996 & 0.997 & 0.994 & 0.997 \\ |
1466 |
& 0.3 & 0.955 & 0.966 & 0.984 & 0.992 & 0.978 & 0.991 \\ |
1467 |
GSC & & 0.964 & 0.731 & 0.984 & 0.704 & 1.005 & 0.770 \\ |
1468 |
RF & & 0.968 & 0.605 & 0.974 & 0.541 & 1.014 & 0.614 \\ |
1469 |
\midrule |
1470 |
PC & & 1.354 & 0.000 & -1.190 & 0.000 & -0.314 & 0.000 \\ |
1471 |
SP & 0.0 & 0.720 & 0.338 & 0.808 & 0.523 & 0.860 & 0.643 \\ |
1472 |
& 0.1 & 0.839 & 0.583 & 0.955 & 0.882 & 0.992 & 0.978 \\ |
1473 |
& 0.2 & 0.995 & 0.987 & 0.999 & 1.000 & 0.999 & 1.000 \\ |
1474 |
& 0.3 & 0.995 & 0.996 & 0.996 & 0.998 & 0.996 & 0.998 \\ |
1475 |
SF & 0.0 & 0.998 & 0.994 & 1.000 & 0.998 & 1.000 & 0.999 \\ |
1476 |
& 0.1 & 0.997 & 0.994 & 1.000 & 0.999 & 1.000 & 1.000 \\ |
1477 |
& 0.2 & 0.999 & 0.998 & 0.999 & 1.000 & 0.999 & 1.000 \\ |
1478 |
& 0.3 & 0.995 & 0.996 & 0.996 & 0.998 & 0.996 & 0.998 \\ |
1479 |
GSC & & 0.995 & 0.990 & 0.998 & 0.997 & 0.998 & 0.996 \\ |
1480 |
RF & & 0.998 & 0.993 & 0.999 & 0.998 & 0.999 & 0.996 \\ |
1481 |
\midrule |
1482 |
PC & & 2.437 & 0.000 & -1.872 & 0.000 & 2.138 & 0.000 \\ |
1483 |
SP & 0.0 & 0.838 & 0.525 & 0.901 & 0.686 & 0.932 & 0.779 \\ |
1484 |
& 0.1 & 0.914 & 0.733 & 0.979 & 0.932 & 0.995 & 0.987 \\ |
1485 |
& 0.2 & 0.977 & 0.969 & 0.988 & 0.990 & 0.989 & 0.990 \\ |
1486 |
& 0.3 & 0.952 & 0.950 & 0.964 & 0.971 & 0.965 & 0.970 \\ |
1487 |
SF & 0.0 & 0.969 & 0.977 & 0.987 & 0.996 & 0.993 & 0.998 \\ |
1488 |
& 0.1 & 0.975 & 0.978 & 0.993 & 0.996 & 0.997 & 0.998 \\ |
1489 |
& 0.2 & 0.976 & 0.973 & 0.988 & 0.990 & 0.989 & 0.990 \\ |
1490 |
& 0.3 & 0.952 & 0.950 & 0.964 & 0.971 & 0.965 & 0.970 \\ |
1491 |
GSC & & 0.980 & 0.959 & 0.990 & 0.983 & 0.992 & 0.989 \\ |
1492 |
RF & & 0.984 & 0.975 & 0.996 & 0.995 & 0.998 & 0.998 \\ |
1493 |
\bottomrule |
1494 |
\end{tabular} |
1495 |
\label{tab:solnWeak} |
1496 |
\end{table} |
1497 |
|
1498 |
\begin{table}[htbp] |
1499 |
\centering |
1500 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR |
1501 |
DISTRIBUTIONS OF THE FORCE AND TORQUE VECTORS IN THE WEAK SODIUM |
1502 |
CHLORIDE SOLUTION SYSTEM} |
1503 |
|
1504 |
\footnotesize |
1505 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1506 |
\toprule |
1507 |
\toprule |
1508 |
& & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\ |
1509 |
\cmidrule(lr){3-5} |
1510 |
\cmidrule(l){6-8} |
1511 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA & 9\AA & 12\AA & 15\AA \\ |
1512 |
\midrule |
1513 |
PC & & 882.863 & 510.435 & 344.201 & 277.691 & 154.231 & 100.131 \\ |
1514 |
SP & 0.0 & 732.569 & 405.704 & 257.756 & 261.445 & 142.245 & 91.497 \\ |
1515 |
& 0.1 & 329.031 & 70.746 & 12.014 & 118.496 & 25.218 & 4.711 \\ |
1516 |
& 0.2 & 6.772 & 0.153 & 0.118 & 9.780 & 2.101 & 2.102 \\ |
1517 |
& 0.3 & 0.951 & 0.774 & 0.784 & 12.108 & 7.673 & 7.851 \\ |
1518 |
SF & 0.0 & 2.555 & 0.762 & 0.313 & 6.590 & 1.328 & 0.558 \\ |
1519 |
& 0.1 & 2.561 & 0.560 & 0.123 & 6.464 & 1.162 & 0.457 \\ |
1520 |
& 0.2 & 0.501 & 0.118 & 0.118 & 5.698 & 2.074 & 2.099 \\ |
1521 |
& 0.3 & 0.943 & 0.774 & 0.784 & 12.118 & 7.674 & 7.851 \\ |
1522 |
GSC & & 2.915 & 0.643 & 0.261 & 9.576 & 3.133 & 1.812 \\ |
1523 |
RF & & 2.415 & 0.452 & 0.130 & 6.915 & 1.423 & 0.507 \\ |
1524 |
\midrule |
1525 |
GSSP & 0.0 & 2.915 & 0.643 & 0.261 & 9.576 & 3.133 & 1.812 \\ |
1526 |
& 0.1 & 2.251 & 0.324 & 0.064 & 7.628 & 1.639 & 0.497 \\ |
1527 |
& 0.2 & 0.590 & 0.118 & 0.116 & 6.080 & 2.096 & 2.103 \\ |
1528 |
& 0.3 & 0.953 & 0.759 & 0.780 & 12.347 & 7.683 & 7.849 \\ |
1529 |
GSSF & 0.0 & 1.541 & 0.301 & 0.096 & 6.407 & 1.316 & 0.496 \\ |
1530 |
& 0.1 & 1.541 & 0.237 & 0.050 & 6.356 & 1.202 & 0.457 \\ |
1531 |
& 0.2 & 0.568 & 0.118 & 0.116 & 6.166 & 2.105 & 2.105 \\ |
1532 |
& 0.3 & 0.954 & 0.759 & 0.780 & 12.337 & 7.684 & 7.849 \\ |
1533 |
\bottomrule |
1534 |
\end{tabular} |
1535 |
\label{tab:solnWeakAng} |
1536 |
\end{table} |
1537 |
|
1538 |
Because this system is a perturbation of the pure liquid water system, |
1539 |
comparisons are best drawn between these two sets. The {\sc sp} and |
1540 |
{\sc sf} methods are not significantly affected by the inclusion of a |
1541 |
few ions. The aspect of cutoff sphere neutralization aids in the |
1542 |
smooth incorporation of these ions; thus, all of the observations |
1543 |
regarding these methods carry over from section |
1544 |
\ref{sec:WaterResults}. The differences between these systems are more |
1545 |
visible for the {\sc rf} method. Though good force agreement is still |
1546 |
maintained, the energy gaps show a significant increase in the scatter |
1547 |
of the data. |
1548 |
|
1549 |
\subsection{1.1M NaCl Solution Results} |
1550 |
|
1551 |
The bridging of the charged atomic and neutral molecular systems was |
1552 |
further developed by considering a high ionic strength system |
1553 |
consisting of 40 ions in the 1000 SPC/E water solvent ($\approx$1.1 |
1554 |
M). The results for the energy gap comparisons and the force and |
1555 |
torque vector magnitude comparisons are shown in table |
1556 |
\ref{tab:solnStr}. The force and torque vector directionality |
1557 |
results are displayed separately in table \ref{tab:solnStrAng}, where |
1558 |
the effect of group-based cutoffs and switching functions on the {\sc |
1559 |
sp} and {\sc sf} potentials are investigated. |
1560 |
|
1561 |
\begin{table}[htbp] |
1562 |
\centering |
1563 |
\caption{REGRESSION RESULTS OF THE STRONG SODIUM CHLORIDE SOLUTION |
1564 |
SYSTEM FOR $\Delta E$ VALUES ({\it upper}), FORCE VECTOR MAGNITUDES |
1565 |
({\it middle}) AND TORQUE VECTOR MAGNITUDES ({\it lower})} |
1566 |
|
1567 |
\footnotesize |
1568 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1569 |
\toprule |
1570 |
\toprule |
1571 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1572 |
\cmidrule(lr){3-4} |
1573 |
\cmidrule(lr){5-6} |
1574 |
\cmidrule(l){7-8} |
1575 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1576 |
\midrule |
1577 |
PC & & -0.081 & 0.000 & 0.945 & 0.001 & 0.073 & 0.000 \\ |
1578 |
SP & 0.0 & 0.978 & 0.469 & 0.996 & 0.672 & 0.975 & 0.668 \\ |
1579 |
& 0.1 & 0.944 & 0.645 & 0.997 & 0.886 & 0.991 & 0.978 \\ |
1580 |
& 0.2 & 0.873 & 0.896 & 0.985 & 0.993 & 0.980 & 0.993 \\ |
1581 |
& 0.3 & 0.831 & 0.860 & 0.960 & 0.979 & 0.955 & 0.977 \\ |
1582 |
SF & 0.0 & 0.858 & 0.905 & 0.985 & 0.970 & 0.990 & 0.998 \\ |
1583 |
& 0.1 & 0.865 & 0.907 & 0.992 & 0.974 & 0.994 & 0.999 \\ |
1584 |
& 0.2 & 0.862 & 0.894 & 0.985 & 0.993 & 0.980 & 0.993 \\ |
1585 |
& 0.3 & 0.831 & 0.859 & 0.960 & 0.979 & 0.955 & 0.977 \\ |
1586 |
GSC & & 1.985 & 0.152 & 0.760 & 0.031 & 1.106 & 0.062 \\ |
1587 |
RF & & 2.414 & 0.116 & 0.813 & 0.017 & 1.434 & 0.047 \\ |
1588 |
\midrule |
1589 |
PC & & -7.028 & 0.000 & -9.364 & 0.000 & 0.925 & 0.865 \\ |
1590 |
SP & 0.0 & 0.701 & 0.319 & 0.909 & 0.773 & 0.861 & 0.665 \\ |
1591 |
& 0.1 & 0.824 & 0.565 & 0.970 & 0.930 & 0.990 & 0.979 \\ |
1592 |
& 0.2 & 0.988 & 0.981 & 0.995 & 0.998 & 0.991 & 0.998 \\ |
1593 |
& 0.3 & 0.983 & 0.985 & 0.985 & 0.991 & 0.978 & 0.990 \\ |
1594 |
SF & 0.0 & 0.993 & 0.988 & 0.992 & 0.984 & 0.998 & 0.999 \\ |
1595 |
& 0.1 & 0.993 & 0.989 & 0.993 & 0.986 & 0.998 & 1.000 \\ |
1596 |
& 0.2 & 0.993 & 0.992 & 0.995 & 0.998 & 0.991 & 0.998 \\ |
1597 |
& 0.3 & 0.983 & 0.985 & 0.985 & 0.991 & 0.978 & 0.990 \\ |
1598 |
GSC & & 0.964 & 0.897 & 0.970 & 0.917 & 0.925 & 0.865 \\ |
1599 |
RF & & 0.994 & 0.864 & 0.988 & 0.865 & 0.980 & 0.784 \\ |
1600 |
\midrule |
1601 |
PC & & -2.212 & 0.000 & -0.588 & 0.000 & 0.953 & 0.925 \\ |
1602 |
SP & 0.0 & 0.800 & 0.479 & 0.930 & 0.804 & 0.924 & 0.759 \\ |
1603 |
& 0.1 & 0.883 & 0.694 & 0.976 & 0.942 & 0.993 & 0.986 \\ |
1604 |
& 0.2 & 0.952 & 0.943 & 0.980 & 0.984 & 0.980 & 0.983 \\ |
1605 |
& 0.3 & 0.914 & 0.909 & 0.943 & 0.948 & 0.944 & 0.946 \\ |
1606 |
SF & 0.0 & 0.945 & 0.953 & 0.980 & 0.984 & 0.991 & 0.998 \\ |
1607 |
& 0.1 & 0.951 & 0.954 & 0.987 & 0.986 & 0.995 & 0.998 \\ |
1608 |
& 0.2 & 0.951 & 0.946 & 0.980 & 0.984 & 0.980 & 0.983 \\ |
1609 |
& 0.3 & 0.914 & 0.908 & 0.943 & 0.948 & 0.944 & 0.946 \\ |
1610 |
GSC & & 0.882 & 0.818 & 0.939 & 0.902 & 0.953 & 0.925 \\ |
1611 |
RF & & 0.949 & 0.939 & 0.988 & 0.988 & 0.992 & 0.993 \\ |
1612 |
\bottomrule |
1613 |
\end{tabular} |
1614 |
\label{tab:solnStr} |
1615 |
\end{table} |
1616 |
|
1617 |
\begin{table}[htbp] |
1618 |
\centering |
1619 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR DISTRIBUTIONS |
1620 |
OF THE FORCE AND TORQUE VECTORS IN THE STRONG SODIUM CHLORIDE SOLUTION |
1621 |
SYSTEM} |
1622 |
|
1623 |
\footnotesize |
1624 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1625 |
\toprule |
1626 |
\toprule |
1627 |
& & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\ |
1628 |
\cmidrule(lr){3-5} |
1629 |
\cmidrule(l){6-8} |
1630 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA & 9\AA & 12\AA & 15\AA \\ |
1631 |
\midrule |
1632 |
PC & & 957.784 & 513.373 & 2.260 & 340.043 & 179.443 & 13.079 \\ |
1633 |
SP & 0.0 & 786.244 & 139.985 & 259.289 & 311.519 & 90.280 & 105.187 \\ |
1634 |
& 0.1 & 354.697 & 38.614 & 12.274 & 144.531 & 23.787 & 5.401 \\ |
1635 |
& 0.2 & 7.674 & 0.363 & 0.215 & 16.655 & 3.601 & 3.634 \\ |
1636 |
& 0.3 & 1.745 & 1.456 & 1.449 & 23.669 & 14.376 & 14.240 \\ |
1637 |
SF & 0.0 & 3.282 & 8.567 & 0.369 & 11.904 & 6.589 & 0.717 \\ |
1638 |
& 0.1 & 3.263 & 7.479 & 0.142 & 11.634 & 5.750 & 0.591 \\ |
1639 |
& 0.2 & 0.686 & 0.324 & 0.215 & 10.809 & 3.580 & 3.635 \\ |
1640 |
& 0.3 & 1.749 & 1.456 & 1.449 & 23.635 & 14.375 & 14.240 \\ |
1641 |
GSC & & 6.181 & 2.904 & 2.263 & 44.349 & 19.442 & 12.873 \\ |
1642 |
RF & & 3.891 & 0.847 & 0.323 & 18.628 & 3.995 & 2.072 \\ |
1643 |
\midrule |
1644 |
GSSP & 0.0 & 6.197 & 2.929 & 2.290 & 44.441 & 19.442 & 12.873 \\ |
1645 |
& 0.1 & 4.688 & 1.064 & 0.260 & 31.208 & 6.967 & 2.303 \\ |
1646 |
& 0.2 & 1.021 & 0.218 & 0.213 & 14.425 & 3.629 & 3.649 \\ |
1647 |
& 0.3 & 1.752 & 1.454 & 1.451 & 23.540 & 14.390 & 14.245 \\ |
1648 |
GSSF & 0.0 & 2.494 & 0.546 & 0.217 & 16.391 & 3.230 & 1.613 \\ |
1649 |
& 0.1 & 2.448 & 0.429 & 0.106 & 16.390 & 2.827 & 1.159 \\ |
1650 |
& 0.2 & 0.899 & 0.214 & 0.213 & 13.542 & 3.583 & 3.645 \\ |
1651 |
& 0.3 & 1.752 & 1.454 & 1.451 & 23.587 & 14.390 & 14.245 \\ |
1652 |
\bottomrule |
1653 |
\end{tabular} |
1654 |
\label{tab:solnStrAng} |
1655 |
\end{table} |
1656 |
|
1657 |
The {\sc rf} method struggles with the jump in ionic strength. The |
1658 |
configuration energy differences degrade to unusable levels while the |
1659 |
forces and torques show a more modest reduction in the agreement with |
1660 |
{\sc spme}. The {\sc rf} method was designed for homogeneous systems, |
1661 |
and this attribute is apparent in these results. |
1662 |
|
1663 |
The {\sc sp} and {\sc sf} methods require larger cutoffs to maintain |
1664 |
their agreement with {\sc spme}. With these results, we still |
1665 |
recommend undamped to moderate damping for the {\sc sf} method and |
1666 |
moderate damping for the {\sc sp} method, both with cutoffs greater |
1667 |
than 12\AA. |
1668 |
|
1669 |
\subsection{6\AA\ Argon Sphere in SPC/E Water Results} |
1670 |
|
1671 |
The final model system studied was a 6\AA\ sphere of Argon solvated |
1672 |
by SPC/E water. This serves as a test case of a specifically sized |
1673 |
electrostatic defect in a disordered molecular system. The results for |
1674 |
the energy gap comparisons and the force and torque vector magnitude |
1675 |
comparisons are shown in table \ref{tab:argon}. The force and torque |
1676 |
vector directionality results are displayed separately in table |
1677 |
\ref{tab:argonAng}, where the effect of group-based cutoffs and |
1678 |
switching functions on the {\sc sp} and {\sc sf} potentials are |
1679 |
investigated. |
1680 |
|
1681 |
\begin{table}[htbp] |
1682 |
\centering |
1683 |
\caption{REGRESSION RESULTS OF THE 6\AA\ ARGON SPHERE IN LIQUID |
1684 |
WATER SYSTEM FOR $\Delta E$ VALUES ({\it upper}), FORCE VECTOR |
1685 |
MAGNITUDES ({\it middle}) AND TORQUE VECTOR MAGNITUDES ({\it lower})} |
1686 |
|
1687 |
\footnotesize |
1688 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1689 |
\toprule |
1690 |
\toprule |
1691 |
& & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\ |
1692 |
\cmidrule(lr){3-4} |
1693 |
\cmidrule(lr){5-6} |
1694 |
\cmidrule(l){7-8} |
1695 |
Method & $\alpha$ & slope & $R^2$ & slope & $R^2$ & slope & $R^2$ \\ |
1696 |
\midrule |
1697 |
PC & & 2.320 & 0.008 & -0.650 & 0.001 & 3.848 & 0.029 \\ |
1698 |
SP & 0.0 & 1.053 & 0.711 & 0.977 & 0.820 & 0.974 & 0.882 \\ |
1699 |
& 0.1 & 1.032 & 0.846 & 0.989 & 0.965 & 0.992 & 0.994 \\ |
1700 |
& 0.2 & 0.993 & 0.995 & 0.982 & 0.998 & 0.986 & 0.998 \\ |
1701 |
& 0.3 & 0.968 & 0.995 & 0.954 & 0.992 & 0.961 & 0.994 \\ |
1702 |
SF & 0.0 & 0.982 & 0.996 & 0.992 & 0.999 & 0.993 & 1.000 \\ |
1703 |
& 0.1 & 0.987 & 0.996 & 0.996 & 0.999 & 0.997 & 1.000 \\ |
1704 |
& 0.2 & 0.989 & 0.998 & 0.984 & 0.998 & 0.989 & 0.998 \\ |
1705 |
& 0.3 & 0.971 & 0.995 & 0.957 & 0.992 & 0.965 & 0.994 \\ |
1706 |
GSC & & 1.002 & 0.983 & 0.992 & 0.973 & 0.996 & 0.971 \\ |
1707 |
RF & & 0.998 & 0.995 & 0.999 & 0.998 & 0.998 & 0.998 \\ |
1708 |
\midrule |
1709 |
PC & & -36.559 & 0.002 & -44.917 & 0.004 & -52.945 & 0.006 \\ |
1710 |
SP & 0.0 & 0.890 & 0.786 & 0.927 & 0.867 & 0.949 & 0.909 \\ |
1711 |
& 0.1 & 0.942 & 0.895 & 0.984 & 0.974 & 0.997 & 0.995 \\ |
1712 |
& 0.2 & 0.999 & 0.997 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1713 |
& 0.3 & 1.001 & 0.999 & 1.001 & 1.000 & 1.001 & 1.000 \\ |
1714 |
SF & 0.0 & 1.000 & 0.999 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1715 |
& 0.1 & 1.000 & 0.999 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1716 |
& 0.2 & 1.000 & 1.000 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1717 |
& 0.3 & 1.001 & 0.999 & 1.001 & 1.000 & 1.001 & 1.000 \\ |
1718 |
GSC & & 0.999 & 0.999 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1719 |
RF & & 0.999 & 0.999 & 1.000 & 1.000 & 1.000 & 1.000 \\ |
1720 |
\midrule |
1721 |
PC & & 1.984 & 0.000 & 0.012 & 0.000 & 1.357 & 0.000 \\ |
1722 |
SP & 0.0 & 0.850 & 0.552 & 0.907 & 0.703 & 0.938 & 0.793 \\ |
1723 |
& 0.1 & 0.924 & 0.755 & 0.980 & 0.936 & 0.995 & 0.988 \\ |
1724 |
& 0.2 & 0.985 & 0.983 & 0.986 & 0.988 & 0.987 & 0.988 \\ |
1725 |
& 0.3 & 0.961 & 0.966 & 0.959 & 0.964 & 0.960 & 0.966 \\ |
1726 |
SF & 0.0 & 0.977 & 0.989 & 0.987 & 0.995 & 0.992 & 0.998 \\ |
1727 |
& 0.1 & 0.982 & 0.989 & 0.992 & 0.996 & 0.997 & 0.998 \\ |
1728 |
& 0.2 & 0.984 & 0.987 & 0.986 & 0.987 & 0.987 & 0.988 \\ |
1729 |
& 0.3 & 0.961 & 0.966 & 0.959 & 0.964 & 0.960 & 0.966 \\ |
1730 |
GSC & & 0.995 & 0.981 & 0.999 & 0.990 & 1.000 & 0.993 \\ |
1731 |
RF & & 0.993 & 0.988 & 0.997 & 0.995 & 0.999 & 0.998 \\ |
1732 |
\bottomrule |
1733 |
\end{tabular} |
1734 |
\label{tab:argon} |
1735 |
\end{table} |
1736 |
|
1737 |
\begin{table}[htbp] |
1738 |
\centering |
1739 |
\caption{VARIANCE RESULTS FROM GAUSSIAN FITS TO ANGULAR |
1740 |
DISTRIBUTIONS OF THE FORCE AND TORQUE VECTORS IN THE 6\AA\ SPHERE OF |
1741 |
ARGON IN LIQUID WATER SYSTEM} |
1742 |
|
1743 |
\footnotesize |
1744 |
\begin{tabular}{@{} ccrrrrrr @{}} |
1745 |
\toprule |
1746 |
\toprule |
1747 |
& & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\ |
1748 |
\cmidrule(lr){3-5} |
1749 |
\cmidrule(l){6-8} |
1750 |
Method & $\alpha$ & 9\AA & 12\AA & 15\AA & 9\AA & 12\AA & 15\AA \\ |
1751 |
\midrule |
1752 |
PC & & 568.025 & 265.993 & 195.099 & 246.626 & 138.600 & 91.654 \\ |
1753 |
SP & 0.0 & 504.578 & 251.694 & 179.932 & 231.568 & 131.444 & 85.119 \\ |
1754 |
& 0.1 & 224.886 & 49.746 & 9.346 & 104.482 & 23.683 & 4.480 \\ |
1755 |
& 0.2 & 4.889 & 0.197 & 0.155 & 6.029 & 2.507 & 2.269 \\ |
1756 |
& 0.3 & 0.817 & 0.833 & 0.812 & 8.286 & 8.436 & 8.135 \\ |
1757 |
SF & 0.0 & 1.924 & 0.675 & 0.304 & 3.658 & 1.448 & 0.600 \\ |
1758 |
& 0.1 & 1.937 & 0.515 & 0.143 & 3.565 & 1.308 & 0.546 \\ |
1759 |
& 0.2 & 0.407 & 0.166 & 0.156 & 3.086 & 2.501 & 2.274 \\ |
1760 |
& 0.3 & 0.815 & 0.833 & 0.812 & 8.330 & 8.437 & 8.135 \\ |
1761 |
GSC & & 2.098 & 0.584 & 0.284 & 5.391 & 2.414 & 1.501 \\ |
1762 |
RF & & 1.822 & 0.408 & 0.142 & 3.799 & 1.362 & 0.550 \\ |
1763 |
\midrule |
1764 |
GSSP & 0.0 & 2.098 & 0.584 & 0.284 & 5.391 & 2.414 & 1.501 \\ |
1765 |
& 0.1 & 1.652 & 0.309 & 0.087 & 4.197 & 1.401 & 0.590 \\ |
1766 |
& 0.2 & 0.465 & 0.165 & 0.153 & 3.323 & 2.529 & 2.273 \\ |
1767 |
& 0.3 & 0.813 & 0.825 & 0.816 & 8.316 & 8.447 & 8.132 \\ |
1768 |
GSSF & 0.0 & 1.173 & 0.292 & 0.113 & 3.452 & 1.347 & 0.583 \\ |
1769 |
& 0.1 & 1.166 & 0.240 & 0.076 & 3.381 & 1.281 & 0.575 \\ |
1770 |
& 0.2 & 0.459 & 0.165 & 0.153 & 3.430 & 2.542 & 2.273 \\ |
1771 |
& 0.3 & 0.814 & 0.825 & 0.816 & 8.325 & 8.447 & 8.132 \\ |
1772 |
\bottomrule |
1773 |
\end{tabular} |
1774 |
\label{tab:argonAng} |
1775 |
\end{table} |
1776 |
|
1777 |
This system does not appear to show any significant deviations from |
1778 |
the previously observed results. The {\sc sp} and {\sc sf} methods |
1779 |
have agreements similar to those observed in section |
1780 |
\ref{sec:WaterResults}. The only significant difference is the |
1781 |
improvement in the configuration energy differences for the {\sc rf} |
1782 |
method. This is surprising in that we are introducing an inhomogeneity |
1783 |
to the system; however, this inhomogeneity is charge-neutral and does |
1784 |
not result in charged cutoff spheres. The charge-neutrality of the |
1785 |
cutoff spheres, which the {\sc sp} and {\sc sf} methods explicitly |
1786 |
enforce, seems to play a greater role in the stability of the {\sc rf} |
1787 |
method than the required homogeneity of the environment. |
1788 |
|
1789 |
|
1790 |
\section{Short-Time Dynamics: Velocity Autocorrelation Functions of NaCl Crystals}\label{sec:ShortTimeDynamics} |
1791 |
|
1792 |
Zahn {\it et al.} investigated the structure and dynamics of water |
1793 |
using equations (\ref{eq:ZahnPot}) and |
1794 |
(\ref{eq:WolfForces}).\cite{Zahn02,Kast03} Their results indicated |
1795 |
that a method similar (but not identical with) the damped {\sc sf} |
1796 |
method resulted in properties very similar to those obtained when |
1797 |
using the Ewald summation. The properties they studied (pair |
1798 |
distribution functions, diffusion constants, and velocity and |
1799 |
orientational correlation functions) may not be particularly sensitive |
1800 |
to the long-range and collective behavior that governs the |
1801 |
low-frequency behavior in crystalline systems. Additionally, the |
1802 |
ionic crystals are the worst case scenario for the pairwise methods |
1803 |
because they lack the reciprocal space contribution contained in the |
1804 |
Ewald summation. |
1805 |
|
1806 |
We are using two separate measures to probe the effects of these |
1807 |
alternative electrostatic methods on the dynamics in crystalline |
1808 |
materials. For short- and intermediate-time dynamics, we are |
1809 |
computing the velocity autocorrelation function, and for long-time |
1810 |
and large length-scale collective motions, we are looking at the |
1811 |
low-frequency portion of the power spectrum. |
1812 |
|
1813 |
\begin{figure} |
1814 |
\centering |
1815 |
\includegraphics[width = \linewidth]{./figures/vCorrPlot.pdf} |
1816 |
\caption{Velocity autocorrelation functions of NaCl crystals at |
1817 |
1000K using {\sc spme}, {\sc sf} ($\alpha$ = 0.0, 0.1, \& |
1818 |
0.2\AA$^{-1}$), and {\sc sp} ($\alpha$ = 0.2\AA$^{-1}$). The inset is |
1819 |
a magnification of the area around the first minimum. The times to |
1820 |
first collision are nearly identical, but differences can be seen in |
1821 |
the peaks and troughs, where the undamped and weakly damped methods |
1822 |
are stiffer than the moderately damped and {\sc spme} methods.} |
1823 |
\label{fig:vCorrPlot} |
1824 |
\end{figure} |
1825 |
|
1826 |
The short-time decay of the velocity autocorrelation function through |
1827 |
the first collision are nearly identical in figure |
1828 |
\ref{fig:vCorrPlot}, but the peaks and troughs of the functions show |
1829 |
how the methods differ. The undamped {\sc sf} method has deeper |
1830 |
troughs (see inset in Fig. \ref{fig:vCorrPlot}) and higher peaks than |
1831 |
any of the other methods. As the damping parameter ($\alpha$) is |
1832 |
increased, these peaks are smoothed out, and the {\sc sf} method |
1833 |
approaches the {\sc spme} results. With $\alpha$ values of 0.2\AA$^{-1}$, |
1834 |
the {\sc sf} and {\sc sp} functions are nearly identical and track the |
1835 |
{\sc spme} features quite well. This is not surprising because the {\sc sf} |
1836 |
and {\sc sp} potentials become nearly identical with increased |
1837 |
damping. However, this appears to indicate that once damping is |
1838 |
utilized, the details of the form of the potential (and forces) |
1839 |
constructed out of the damped electrostatic interaction are less |
1840 |
important. |
1841 |
|
1842 |
\section{Collective Motion: Power Spectra of NaCl Crystals}\label{sec:LongTimeDynamics} |
1843 |
|
1844 |
To evaluate how the differences between the methods affect the |
1845 |
collective long-time motion, we computed power spectra from long-time |
1846 |
traces of the velocity autocorrelation function. The power spectra for |
1847 |
the best-performing alternative methods are shown in |
1848 |
fig. \ref{fig:methodPS}. Apodization of the correlation functions via |
1849 |
a cubic switching function between 40 and 50ps was used to reduce the |
1850 |
ringing resulting from data truncation. This procedure had no |
1851 |
noticeable effect on peak location or magnitude. |
1852 |
|
1853 |
\begin{figure} |
1854 |
\centering |
1855 |
\includegraphics[width = \linewidth]{./figures/spectraSquare.pdf} |
1856 |
\caption{Power spectra obtained from the velocity auto-correlation |
1857 |
functions of NaCl crystals at 1000K while using {\sc spme}, {\sc sf} |
1858 |
($\alpha$ = 0, 0.1, \& 0.2\AA$^{-1}$), and {\sc sp} ($\alpha$ = |
1859 |
0.2\AA$^{-1}$). The inset shows the frequency region below 100 |
1860 |
cm$^{-1}$ to highlight where the spectra differ.} |
1861 |
\label{fig:methodPS} |
1862 |
\end{figure} |
1863 |
|
1864 |
While the high frequency regions of the power spectra for the |
1865 |
alternative methods are quantitatively identical with Ewald spectrum, |
1866 |
the low frequency region shows how the summation methods differ. |
1867 |
Considering the low-frequency inset (expanded in the upper frame of |
1868 |
figure \ref{fig:dampInc}), at frequencies below 100 cm$^{-1}$, the |
1869 |
correlated motions are blue-shifted when using undamped or weakly |
1870 |
damped {\sc sf}. When using moderate damping ($\alpha = 0.2$ |
1871 |
\AA$^{-1}$) both the {\sc sf} and {\sc sp} methods give nearly identical |
1872 |
correlated motion to the Ewald method (which has a convergence |
1873 |
parameter of 0.3119\AA$^{-1}$). This weakening of the electrostatic |
1874 |
interaction with increased damping explains why the long-ranged |
1875 |
correlated motions are at lower frequencies for the moderately damped |
1876 |
methods than for undamped or weakly damped methods. |
1877 |
|
1878 |
To isolate the role of the damping constant, we have computed the |
1879 |
spectra for a single method ({\sc sf}) with a range of damping |
1880 |
constants and compared this with the {\sc spme} spectrum. |
1881 |
Fig. \ref{fig:dampInc} shows more clearly that increasing the |
1882 |
electrostatic damping red-shifts the lowest frequency phonon modes. |
1883 |
However, even without any electrostatic damping, the {\sc sf} method |
1884 |
has at most a 10 cm$^{-1}$ error in the lowest frequency phonon mode. |
1885 |
Without the {\sc sf} modifications, an undamped (pure cutoff) method |
1886 |
would predict the lowest frequency peak near 325 cm$^{-1}$. {\it |
1887 |
Most} of the collective behavior in the crystal is accurately captured |
1888 |
using the {\sc sf} method. Quantitative agreement with Ewald can be |
1889 |
obtained using moderate damping in addition to the shifting at the |
1890 |
cutoff distance. |
1891 |
|
1892 |
\begin{figure} |
1893 |
\centering |
1894 |
\includegraphics[width = \linewidth]{./figures/increasedDamping.pdf} |
1895 |
\caption{Effect of damping on the two lowest-frequency phonon modes in |
1896 |
the NaCl crystal at 1000K. The undamped shifted force ({\sc sf}) |
1897 |
method is off by less than 10 cm$^{-1}$, and increasing the |
1898 |
electrostatic damping to 0.25\AA$^{-1}$ gives quantitative agreement |
1899 |
with the power spectrum obtained using the Ewald sum. Over-damping can |
1900 |
result in underestimates of frequencies of the long-wavelength |
1901 |
motions.} |
1902 |
\label{fig:dampInc} |
1903 |
\end{figure} |
1904 |
|
1905 |
\section{An Application: TIP5P-E Water}\label{sec:t5peApplied} |
1906 |
|
1907 |
The above sections focused on the energetics and dynamics of a variety |
1908 |
of systems when utilizing the {\sc sp} and {\sc sf} pairwise |
1909 |
techniques. A unitary correlation with results obtained using the |
1910 |
Ewald summation should result in a successful reproduction of both the |
1911 |
static and dynamic properties of any selected system. To test this, |
1912 |
we decided to calculate a series of properties for the TIP5P-E water |
1913 |
model when using the {\sc sf} technique. |
1914 |
|
1915 |
The TIP5P-E water model is a variant of Mahoney and Jorgensen's |
1916 |
five-point transferable intermolecular potential (TIP5P) model for |
1917 |
water.\cite{Mahoney00} TIP5P was developed to reproduce the density |
1918 |
maximum anomaly present in liquid water near 4$^\circ$C. As with many |
1919 |
previous point charge water models (such as ST2, TIP3P, TIP4P, SPC, |
1920 |
and SPC/E), TIP5P was parametrized using a simple cutoff with no |
1921 |
long-range electrostatic |
1922 |
correction.\cite{Stillinger74,Jorgensen83,Berendsen81,Berendsen87} |
1923 |
Without this correction, the pressure term on the central particle |
1924 |
from the surroundings is missing. Because they expand to compensate |
1925 |
for this added pressure term when this correction is included, systems |
1926 |
composed of these particles tend to under-predict the density of water |
1927 |
under standard conditions. When using any form of long-range |
1928 |
electrostatic correction, it has become common practice to develop or |
1929 |
utilize a reparametrized water model that corrects for this |
1930 |
effect.\cite{vanderSpoel98,Fennell04,Horn04} The TIP5P-E model follows |
1931 |
this practice and was optimized specifically for use with the Ewald |
1932 |
summation.\cite{Rick04} In his publication, Rick preserved the |
1933 |
geometry and point charge magnitudes in TIP5P and focused on altering |
1934 |
the Lennard-Jones parameters to correct the density at |
1935 |
298K.\cite{Rick04} With the density corrected, he compared common |
1936 |
water properties for TIP5P-E using the Ewald sum with TIP5P using a |
1937 |
9\AA\ cutoff. |
1938 |
|
1939 |
In the following sections, we compared these same water properties |
1940 |
calculated from TIP5P-E using the Ewald sum with TIP5P-E using the |
1941 |
{\sc sf} technique. In the above evaluation of the pairwise |
1942 |
techniques, we observed some flexibility in the choice of parameters. |
1943 |
Because of this, the following comparisons include the {\sc sf} |
1944 |
technique with a 12\AA\ cutoff and an $\alpha$ = 0.0, 0.1, and |
1945 |
0.2\AA$^{-1}$, as well as a 9\AA\ cutoff with an $\alpha$ = |
1946 |
0.2\AA$^{-1}$. |
1947 |
|
1948 |
\subsection{Density}\label{sec:t5peDensity} |
1949 |
|
1950 |
As stated previously, the property that prompted the development of |
1951 |
TIP5P-E was the density at 1 atm. The density depends upon the |
1952 |
internal pressure of the system in the $NPT$ ensemble, and the |
1953 |
calculation of the pressure includes a components from both the |
1954 |
kinetic energy and the virial. More specifically, the instantaneous |
1955 |
molecular pressure ($p(t)$) is given by |
1956 |
\begin{equation} |
1957 |
p(t) = \frac{1}{\textrm{d}V}\sum_\mu |
1958 |
\left[\frac{\mathbf{P}_{\mu}^2}{M_{\mu}} |
1959 |
+ \mathbf{R}_{\mu}\cdot\sum_i\mathbf{F}_{\mu i}\right], |
1960 |
\label{eq:MolecularPressure} |
1961 |
\end{equation} |
1962 |
where $V$ is the volume, $\mathbf{P}_{\mu}$ is the momentum of |
1963 |
molecule $\mu$, $\mathbf{R}_\mu$ is the position of the center of mass |
1964 |
($M_\mu$) of molecule $\mu$, and $\mathbf{F}_{\mu i}$ is the force on |
1965 |
atom $i$ of molecule $\mu$.\cite{Melchionna93} The virial term (the |
1966 |
right term in the brackets of equation \ref{eq:MolecularPressure}) is |
1967 |
directly dependent on the interatomic forces. Since the {\sc sp} |
1968 |
method does not modify the forces (see |
1969 |
section. \ref{sec:PairwiseDerivation}), the pressure using {\sc sp} will |
1970 |
be identical to that obtained without an electrostatic correction. |
1971 |
The {\sc sf} method does alter the virial component and, by way of the |
1972 |
modified pressures, should provide densities more in line with those |
1973 |
obtained using the Ewald summation. |
1974 |
|
1975 |
To compare densities, $NPT$ simulations were performed with the same |
1976 |
temperatures as those selected by Rick in his Ewald summation |
1977 |
simulations.\cite{Rick04} In order to improve statistics around the |
1978 |
density maximum, 3ns trajectories were accumulated at 0, 12.5, and |
1979 |
25$^\circ$C, while 2ns trajectories were obtained at all other |
1980 |
temperatures. The average densities were calculated from the later |
1981 |
three-fourths of each trajectory. Similar to Mahoney and Jorgensen's |
1982 |
method for accumulating statistics, these sequences were spliced into |
1983 |
200 segments to calculate the average density and standard deviation |
1984 |
at each temperature.\cite{Mahoney00} |
1985 |
|
1986 |
\begin{figure} |
1987 |
\includegraphics[width=\linewidth]{./figures/tip5peDensities.pdf} |
1988 |
\caption{Density versus temperature for the TIP5P-E water model when |
1989 |
using the Ewald summation (Ref. \cite{Rick04}) and the {\sc sf} method |
1990 |
with various parameters. The pressure term from the image-charge shell |
1991 |
is larger than that provided by the reciprocal-space portion of the |
1992 |
Ewald summation, leading to slightly lower densities. This effect is |
1993 |
more visible with the 9\AA\ cutoff, where the image charges exert a |
1994 |
greater force on the central particle. The error bars for the {\sc sf} |
1995 |
methods show plus or minus the standard deviation of the density |
1996 |
measurement at each temperature.} |
1997 |
\label{fig:t5peDensities} |
1998 |
\end{figure} |
1999 |
|
2000 |
Figure \ref{fig:t5peDensities} shows the densities calculated for |
2001 |
TIP5P-E using differing electrostatic corrections overlaid on the |
2002 |
experimental values.\cite{CRC80} The densities when using the {\sc sf} |
2003 |
technique are close to, though typically lower than, those calculated |
2004 |
while using the Ewald summation. These slightly reduced densities |
2005 |
indicate that the pressure component from the image charges at |
2006 |
R$_\textrm{c}$ is larger than that exerted by the reciprocal-space |
2007 |
portion of the Ewald summation. Bringing the image charges closer to |
2008 |
the central particle by choosing a 9\AA\ R$_\textrm{c}$ (rather than |
2009 |
the preferred 12\AA\ R$_\textrm{c}$) increases the strength of their |
2010 |
interactions, resulting in a further reduction of the densities. |
2011 |
|
2012 |
Because the strength of the image charge interactions has a noticeable |
2013 |
effect on the density, we would expect the use of electrostatic |
2014 |
damping to also play a role in these calculations. Larger values of |
2015 |
$\alpha$ weaken the pair-interactions; and since electrostatic damping |
2016 |
is distance-dependent, force components from the image charges will be |
2017 |
reduced more than those from particles close the the central |
2018 |
charge. This effect is visible in figure \ref{fig:t5peDensities} with |
2019 |
the damped {\sc sf} sums showing slightly higher densities; however, |
2020 |
it is apparent that the choice of cutoff radius plays a much more |
2021 |
important role in the resulting densities. |
2022 |
|
2023 |
As a final note, all of the above density calculations were performed |
2024 |
with systems of 512 water molecules. Rick observed a system sized |
2025 |
dependence of the computed densities when using the Ewald summation, |
2026 |
most likely due to his tying of the convergence parameter to the box |
2027 |
dimensions.\cite{Rick04} For systems of 256 water molecules, the |
2028 |
calculated densities were on average 0.002 to 0.003 g/cm$^3$ lower. A |
2029 |
system size of 256 molecules would force the use of a shorter |
2030 |
R$_\textrm{c}$ when using the {\sc sf} technique, and this would also |
2031 |
lower the densities. Moving to larger systems, as long as the |
2032 |
R$_\textrm{c}$ remains at a fixed value, we would expect the densities |
2033 |
to remain constant. |
2034 |
|
2035 |
\subsection{Liquid Structure}\label{sec:t5peLiqStructure} |
2036 |
|
2037 |
A common function considered when developing and comparing water |
2038 |
models is the oxygen-oxygen radial distribution function |
2039 |
($g_\textrm{OO}(r)$). The $g_\textrm{OO}(r)$ is the probability of |
2040 |
finding a pair of oxygen atoms some distance ($r$) apart relative to a |
2041 |
random distribution at the same density.\cite{Allen87} It is |
2042 |
calculated via |
2043 |
\begin{equation} |
2044 |
g_\textrm{OO}(r) = \frac{V}{N^2}\left\langle\sum_i\sum_{j\ne i} |
2045 |
\delta(\mathbf{r}-\mathbf{r}_{ij})\right\rangle, |
2046 |
\label{eq:GOOofR} |
2047 |
\end{equation} |
2048 |
where the double sum is over all $i$ and $j$ pairs of $N$ oxygen |
2049 |
atoms. The $g_\textrm{OO}(r)$ can be directly compared to X-ray or |
2050 |
neutron scattering experiments through the oxygen-oxygen structure |
2051 |
factor ($S_\textrm{OO}(k)$) by the following relationship: |
2052 |
\begin{equation} |
2053 |
S_\textrm{OO}(k) = 1 + 4\pi\rho |
2054 |
\int_0^\infty r^2\frac{\sin kr}{kr}g_\textrm{OO}(r)\textrm{d}r. |
2055 |
\label{eq:SOOofK} |
2056 |
\end{equation} |
2057 |
Thus, $S_\textrm{OO}(k)$ is related to the Fourier-Laplace transform |
2058 |
of $g_\textrm{OO}(r)$. |
2059 |
|
2060 |
The experimentally determined $g_\textrm{OO}(r)$ for liquid water has |
2061 |
been compared in great detail with the various common water models, |
2062 |
and TIP5P was found to be in better agreement than other rigid, |
2063 |
non-polarizable models.\cite{Sorenson00} This excellent agreement with |
2064 |
experiment was maintained when Rick developed TIP5P-E.\cite{Rick04} To |
2065 |
check whether the choice of using the Ewald summation or the {\sc sf} |
2066 |
technique alters the liquid structure, the $g_\textrm{OO}(r)$s at 298K |
2067 |
and 1atm were determined for the systems compared in the previous |
2068 |
section. |
2069 |
|
2070 |
\begin{figure} |
2071 |
\includegraphics[width=\linewidth]{./figures/tip5peGofR.pdf} |
2072 |
\caption{The $g_\textrm{OO}(r)$s calculated for TIP5P-E at 298K and |
2073 |
1atm while using the Ewald summation (Ref. \cite{Rick04}) and the {\sc |
2074 |
sf} technique with varying parameters. Even with the reduced densities |
2075 |
using the {\sc sf} technique, the $g_\textrm{OO}(r)$s are essentially |
2076 |
identical.} |
2077 |
\label{fig:t5peGofRs} |
2078 |
\end{figure} |
2079 |
|
2080 |
The $g_\textrm{OO}(r)$s calculated for TIP5P-E while using the {\sc |
2081 |
sf} technique with a various parameters are overlaid on the |
2082 |
$g_\textrm{OO}(r)$ while using the Ewald summation. The differences in |
2083 |
density do not appear to have any effect on the liquid structure as |
2084 |
the $g_\textrm{OO}(r)$s are indistinguishable. These results indicate |
2085 |
that the $g_\textrm{OO}(r)$ is insensitive to the choice of |
2086 |
electrostatic correction. |
2087 |
|
2088 |
\subsection{Thermodynamic Properties}\label{sec:t5peThermo} |
2089 |
|
2090 |
In addition to the density, there are a variety of thermodynamic |
2091 |
quantities that can be calculated for water and compared directly to |
2092 |
experimental values. Some of these additional quantities include the |
2093 |
latent heat of vaporization ($\Delta H_\textrm{vap}$), the constant |
2094 |
pressure heat capacity ($C_p$), the isothermal compressibility |
2095 |
($\kappa_T$), the thermal expansivity ($\alpha_p$), and the static |
2096 |
dielectric constant ($\epsilon$). All of these properties were |
2097 |
calculated for TIP5P-E with the Ewald summation, so they provide a |
2098 |
good set for comparisons involving the {\sc sf} technique. |
2099 |
|
2100 |
The $\Delta H_\textrm{vap}$ is the enthalpy change required to |
2101 |
transform one mol of substance from the liquid phase to the gas |
2102 |
phase.\cite{Berry00} In molecular simulations, this quantity can be |
2103 |
determined via |
2104 |
\begin{equation} |
2105 |
\begin{split} |
2106 |
\Delta H_\textrm{vap} &= H_\textrm{gas} - H_\textrm{liq.} \\ |
2107 |
&= E_\textrm{gas} - E_\textrm{liq.} |
2108 |
+ p(V_\textrm{gas} - V_\textrm{liq.}) \\ |
2109 |
&\approx -\frac{\langle U_\textrm{liq.}\rangle}{N}+ RT, |
2110 |
\end{split} |
2111 |
\label{eq:DeltaHVap} |
2112 |
\end{equation} |
2113 |
where $E$ is the total energy, $U$ is the potential energy, $p$ is the |
2114 |
pressure, $V$ is the volume, $N$ is the number of molecules, $R$ is |
2115 |
the gas constant, and $T$ is the temperature.\cite{Jorgensen98b} As |
2116 |
seen in the last line of equation (\ref{eq:DeltaHVap}), we can |
2117 |
approximate $\Delta H_\textrm{vap}$ by using the ideal gas for the gas |
2118 |
state. This allows us to cancel the kinetic energy terms, leaving only |
2119 |
the $U_\textrm{liq.}$ term. Additionally, the $pV$ term for the gas is |
2120 |
several orders of magnitude larger than that of the liquid, so we can |
2121 |
neglect the liquid $pV$ term. |
2122 |
|
2123 |
The remaining thermodynamic properties can all be calculated from |
2124 |
fluctuations of the enthalpy, volume, and system dipole |
2125 |
moment.\cite{Allen87} $C_p$ can be calculated from fluctuations in the |
2126 |
enthalpy in constant pressure simulations via |
2127 |
\begin{equation} |
2128 |
\begin{split} |
2129 |
C_p = \left(\frac{\partial H}{\partial T}\right)_{N,p} |
2130 |
= \frac{(\langle H^2\rangle - \langle H\rangle^2)}{Nk_BT^2}, |
2131 |
\end{split} |
2132 |
\label{eq:Cp} |
2133 |
\end{equation} |
2134 |
where $k_B$ is Boltzmann's constant. $\kappa_T$ can be calculated via |
2135 |
\begin{equation} |
2136 |
\begin{split} |
2137 |
\kappa_T = \frac{1}{V}\left(\frac{\partial V}{\partial p}\right)_{N,T} |
2138 |
= \frac{(\langle V^2\rangle_{N,P,T} - \langle V\rangle^2_{N,P,T})} |
2139 |
{k_BT\langle V\rangle_{N,P,T}}, |
2140 |
\end{split} |
2141 |
\label{eq:kappa} |
2142 |
\end{equation} |
2143 |
and $\alpha_p$ can be calculated via |
2144 |
\begin{equation} |
2145 |
\begin{split} |
2146 |
\alpha_p = \frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_{N,P} |
2147 |
= \frac{(\langle VH\rangle_{N,P,T} |
2148 |
- \langle V\rangle_{N,P,T}\langle H\rangle_{N,P,T})} |
2149 |
{k_BT^2\langle V\rangle_{N,P,T}}. |
2150 |
\end{split} |
2151 |
\label{eq:alpha} |
2152 |
\end{equation} |
2153 |
Using the Ewald sum under tin-foil boundary conditions, $\epsilon$ can |
2154 |
be calculated for systems of non-polarizable substances via |
2155 |
\begin{equation} |
2156 |
\epsilon = 1 + \frac{\langle M^2\rangle}{3\epsilon_0k_\textrm{B}TV}, |
2157 |
\label{eq:staticDielectric} |
2158 |
\end{equation} |
2159 |
where $\epsilon_0$ is the permittivity of free space and $\langle |
2160 |
M^2\rangle$ is the fluctuation of the system dipole |
2161 |
moment.\cite{Allen87} The numerator in the fractional term in equation |
2162 |
(\ref{eq:staticDielectric}) is the fluctuation of the simulation-box |
2163 |
dipole moment, identical to the quantity calculated in the |
2164 |
finite-system Kirkwood $g$ factor ($G_k$): |
2165 |
\begin{equation} |
2166 |
G_k = \frac{\langle M^2\rangle}{N\mu^2}, |
2167 |
\label{eq:KirkwoodFactor} |
2168 |
\end{equation} |
2169 |
where $\mu$ is the dipole moment of a single molecule of the |
2170 |
homogeneous system.\cite{Neumann83,Neumann84,Neumann85} The |
2171 |
fluctuation term in both equation (\ref{eq:staticDielectric}) and |
2172 |
\ref{eq:KirkwoodFactor} is calculated as follows, |
2173 |
\begin{equation} |
2174 |
\begin{split} |
2175 |
\langle M^2\rangle &= \langle\bm{M}\cdot\bm{M}\rangle |
2176 |
- \langle\bm{M}\rangle\cdot\langle\bm{M}\rangle \\ |
2177 |
&= \langle M_x^2+M_y^2+M_z^2\rangle |
2178 |
- (\langle M_x\rangle^2 + \langle M_x\rangle^2 |
2179 |
+ \langle M_x\rangle^2). |
2180 |
\end{split} |
2181 |
\label{eq:fluctBoxDipole} |
2182 |
\end{equation} |
2183 |
This fluctuation term can be accumulated during the simulation; |
2184 |
however, it converges rather slowly, thus requiring multi-nanosecond |
2185 |
simulation times.\cite{Horn04} In the case of tin-foil boundary |
2186 |
conditions, the dielectric/surface term of equation (\ref{eq:EwaldSum}) |
2187 |
is equal to zero. Since the {\sc sf} method also lacks this |
2188 |
dielectric/surface term, equation (\ref{eq:staticDielectric}) is still |
2189 |
valid for determining static dielectric constants. |
2190 |
|
2191 |
All of the above properties were calculated from the same trajectories |
2192 |
used to determine the densities in section \ref{sec:t5peDensity} |
2193 |
except for the static dielectric constants. The $\epsilon$ values were |
2194 |
accumulated from 2ns $NVE$ ensemble trajectories with system densities |
2195 |
fixed at the average values from the $NPT$ simulations at each of the |
2196 |
temperatures. The resulting values are displayed in figure |
2197 |
\ref{fig:t5peThermo}. |
2198 |
\begin{figure} |
2199 |
\centering |
2200 |
\includegraphics[width=5.5in]{./figures/t5peThermo.pdf} |
2201 |
\caption{Thermodynamic properties for TIP5P-E using the Ewald summation |
2202 |
and the {\sc sf} techniques along with the experimental values. Units |
2203 |
for the properties are kcal mol$^{-1}$ for $\Delta H_\textrm{vap}$, |
2204 |
cal mol$^{-1}$ K$^{-1}$ for $C_p$, 10$^6$ atm$^{-1}$ for $\kappa_T$, |
2205 |
and 10$^5$ K$^{-1}$ for $\alpha_p$. Ewald summation results are from |
2206 |
reference \cite{Rick04}. Experimental values for $\Delta |
2207 |
H_\textrm{vap}$, $\kappa_T$, and $\alpha_p$ are from reference |
2208 |
\cite{Kell75}. Experimental values for $C_p$ are from reference |
2209 |
\cite{Wagner02}. Experimental values for $\epsilon$ are from reference |
2210 |
\cite{Malmberg56}.} |
2211 |
\label{fig:t5peThermo} |
2212 |
\end{figure} |
2213 |
|
2214 |
As observed for the density in section \ref{sec:t5peDensity}, the |
2215 |
property trends with temperature seen when using the Ewald summation |
2216 |
are reproduced with the {\sc sf} technique. Differences include the |
2217 |
calculated values of $\Delta H_\textrm{vap}$ under-predicting the Ewald |
2218 |
values. This is to be expected due to the direct weakening of the |
2219 |
electrostatic interaction through forced neutralization in {\sc |
2220 |
sf}. This results in an increase of the intermolecular potential |
2221 |
producing lower values from equation (\ref{eq:DeltaHVap}). The slopes of |
2222 |
these values with temperature are similar to that seen using the Ewald |
2223 |
summation; however, they are both steeper than the experimental trend, |
2224 |
indirectly resulting in the inflated $C_p$ values at all temperatures. |
2225 |
|
2226 |
Above the supercooled regime, $C_p$, $\kappa_T$, and $\alpha_p$ |
2227 |
values all overlap within error. As indicated for the $\Delta |
2228 |
H_\textrm{vap}$ and $C_p$ results discussed in the previous paragraph, |
2229 |
the deviations between experiment and simulation in this region are |
2230 |
not the fault of the electrostatic summation methods but are due to |
2231 |
the TIP5P class model itself. Like most rigid, non-polarizable, |
2232 |
point-charge water models, the density decreases with temperature at a |
2233 |
much faster rate than experiment (see figure |
2234 |
\ref{fig:t5peDensities}). The reduced density leads to the inflated |
2235 |
compressibility and expansivity values at higher temperatures seen |
2236 |
here in figure \ref{fig:t5peThermo}. Incorporation of polarizability |
2237 |
and many-body effects are required in order for simulation to overcome |
2238 |
these differences with experiment.\cite{Laasonen93,Donchev06} |
2239 |
|
2240 |
At temperatures below the freezing point for experimental water, the |
2241 |
differences between {\sc sf} and the Ewald summation results are more |
2242 |
apparent. The larger $C_p$ and lower $\alpha_p$ values in this region |
2243 |
indicate a more pronounced transition in the supercooled regime, |
2244 |
particularly in the case of {\sc sf} without damping. This points to |
2245 |
the onset of a more frustrated or glassy behavior for TIP5P-E at |
2246 |
temperatures below 250K in these simulations. Because the systems are |
2247 |
locked in different regions of phase-space, comparisons between |
2248 |
properties at these temperatures are not exactly fair. This |
2249 |
observation is explored in more detail in section |
2250 |
\ref{sec:t5peDynamics}. |
2251 |
|
2252 |
The final thermodynamic property displayed in figure |
2253 |
\ref{fig:t5peThermo}, $\epsilon$, shows the greatest discrepancy |
2254 |
between the Ewald summation and the {\sc sf} technique (and experiment |
2255 |
for that matter). It is known that the dielectric constant is |
2256 |
dependent upon and quite sensitive to the imposed boundary |
2257 |
conditions.\cite{Neumann80,Neumann83} This is readily apparent in the |
2258 |
converged $\epsilon$ values accumulated for the {\sc sf} |
2259 |
simulations. Lack of a damping function results in dielectric |
2260 |
constants significantly smaller than that obtained using the Ewald |
2261 |
sum. Increasing the damping coefficient to 0.2\AA$^{-1}$ improves the |
2262 |
agreement considerably. It should be noted that the choice of the |
2263 |
``Ewald coefficient'' value also has a significant effect on the |
2264 |
calculated value when using the Ewald summation. In the simulations of |
2265 |
TIP5P-E with the Ewald sum, this screening parameter was tethered to |
2266 |
the simulation box size (as was the $R_\textrm{c}$).\cite{Rick04} In |
2267 |
general, systems with larger screening parameters reported larger |
2268 |
dielectric constant values, the same behavior we see here with {\sc |
2269 |
sf}; however, the choice of cutoff radius also plays an important |
2270 |
role. In section \ref{sec:dampingDielectric}, this connection is |
2271 |
further explored as optimal damping coefficients for different choices |
2272 |
of $R_\textrm{c}$ are determined for {\sc sf} for capturing the |
2273 |
dielectric behavior. |
2274 |
|
2275 |
\subsection{Dynamic Properties}\label{sec:t5peDynamics} |
2276 |
|
2277 |
To look at the dynamic properties of TIP5P-E when using the {\sc sf} |
2278 |
method, 200ps $NVE$ simulations were performed for each temperature at |
2279 |
the average density reported by the $NPT$ simulations. The |
2280 |
self-diffusion constants ($D$) were calculated with the Einstein |
2281 |
relation using the mean square displacement (MSD), |
2282 |
\begin{equation} |
2283 |
D = \frac{\langle\left|\mathbf{r}_i(t)-\mathbf{r}_i(0)\right|^2\rangle}{6t}, |
2284 |
\label{eq:MSD} |
2285 |
\end{equation} |
2286 |
where $t$ is time, and $\mathbf{r}_i$ is the position of particle |
2287 |
$i$.\cite{Allen87} Figure \ref{fig:ExampleMSD} shows an example MSD |
2288 |
plot. As labeled in the figure, MSD plots consist of three distinct |
2289 |
regions: |
2290 |
|
2291 |
\begin{enumerate}[itemsep=0pt] |
2292 |
\item parabolic short-time ballistic motion, |
2293 |
\item linear diffusive regime, and |
2294 |
\item poor statistic region at long-time. |
2295 |
\end{enumerate} |
2296 |
The slope from the linear region (region 2) is used to calculate $D$. |
2297 |
\begin{figure} |
2298 |
\centering |
2299 |
\includegraphics[width=3.5in]{./figures/ExampleMSD.pdf} |
2300 |
\caption{Example plot of mean square displacement verses time. The |
2301 |
left red region is the ballistic motion regime, the middle green |
2302 |
region is the linear diffusive regime, and the right blue region is |
2303 |
the region with poor statistics.} |
2304 |
\label{fig:ExampleMSD} |
2305 |
\end{figure} |
2306 |
|
2307 |
\begin{figure} |
2308 |
\centering |
2309 |
\includegraphics[width=3.5in]{./figures/waterFrame.pdf} |
2310 |
\caption{Body-fixed coordinate frame for a water molecule. The |
2311 |
respective molecular principle axes point in the direction of the |
2312 |
labeled frame axes.} |
2313 |
\label{fig:waterFrame} |
2314 |
\end{figure} |
2315 |
In addition to translational diffusion, reorientational time constants |
2316 |
were calculated for comparisons with the Ewald simulations and with |
2317 |
experiments. These values were determined from 25ps $NVE$ trajectories |
2318 |
through calculation of the orientational time correlation function, |
2319 |
\begin{equation} |
2320 |
C_l^\alpha(t) = \left\langle P_l\left[\hat{\mathbf{u}}_i^\alpha(t) |
2321 |
\cdot\hat{\mathbf{u}}_i^\alpha(0)\right]\right\rangle, |
2322 |
\label{eq:OrientCorr} |
2323 |
\end{equation} |
2324 |
where $P_l$ is the Legendre polynomial of order $l$ and |
2325 |
$\hat{\mathbf{u}}_i^\alpha$ is the unit vector of molecule $i$ along |
2326 |
principle axis $\alpha$. The principle axis frame for these water |
2327 |
molecules is shown in figure \ref{fig:waterFrame}. As an example, |
2328 |
$C_l^y$ is calculated from the time evolution of the unit vector |
2329 |
connecting the two hydrogen atoms. |
2330 |
|
2331 |
\begin{figure} |
2332 |
\centering |
2333 |
\includegraphics[width=3.5in]{./figures/ExampleOrientCorr.pdf} |
2334 |
\caption{Example plots of the orientational autocorrelation functions |
2335 |
for the first and second Legendre polynomials. These curves show the |
2336 |
time decay of the unit vector along the $y$ principle axis.} |
2337 |
\label{fig:OrientCorr} |
2338 |
\end{figure} |
2339 |
From the orientation autocorrelation functions, we can obtain time |
2340 |
constants for rotational relaxation. Figure \ref{fig:OrientCorr} shows |
2341 |
some example plots of orientational autocorrelation functions for the |
2342 |
first and second Legendre polynomials. The relatively short time |
2343 |
portions (between 1 and 3ps for water) of these curves can be fit to |
2344 |
an exponential decay to obtain these constants, and they are directly |
2345 |
comparable to water orientational relaxation times from nuclear |
2346 |
magnetic resonance (NMR). The relaxation constant obtained from |
2347 |
$C_2^y(t)$ is of particular interest because it describes the |
2348 |
relaxation of the principle axis connecting the hydrogen atoms. Thus, |
2349 |
$C_2^y(t)$ can be compared to the intermolecular portion of the |
2350 |
dipole-dipole relaxation from a proton NMR signal and should provide |
2351 |
the best estimate of the NMR relaxation time constant.\cite{Impey82} |
2352 |
|
2353 |
\begin{figure} |
2354 |
\centering |
2355 |
\includegraphics[width=5.5in]{./figures/t5peDynamics.pdf} |
2356 |
\caption{Diffusion constants ({\it upper}) and reorientational time |
2357 |
constants ({\it lower}) for TIP5P-E using the Ewald sum and {\sc sf} |
2358 |
technique compared with experiment. Data at temperatures less that |
2359 |
0$^\circ$C were not included in the $\tau_2^y$ plot to allow for |
2360 |
easier comparisons in the more relevant temperature regime.} |
2361 |
\label{fig:t5peDynamics} |
2362 |
\end{figure} |
2363 |
Results for the diffusion constants and reorientational time constants |
2364 |
are shown in figure \ref{fig:t5peDynamics}. From this figure, it is |
2365 |
apparent that the trends for both $D$ and $\tau_2^y$ of TIP5P-E using |
2366 |
the Ewald sum are reproduced with the {\sc sf} technique. The enhanced |
2367 |
diffusion at high temperatures are again the product of the lower |
2368 |
densities in comparison with experiment and do not provide any special |
2369 |
insight into differences between the electrostatic summation |
2370 |
techniques. With the undamped {\sc sf} technique, TIP5P-E tends to |
2371 |
diffuse a little faster than with the Ewald sum; however, use of light |
2372 |
to moderate damping results in indistinguishable $D$ values. Though not |
2373 |
apparent in this figure, {\sc sf} values at the lowest temperature are |
2374 |
approximately an order of magnitude lower than with Ewald. These |
2375 |
values support the observation from section \ref{sec:t5peThermo} that |
2376 |
there appeared to be a change to a more glassy-like phase with the |
2377 |
{\sc sf} technique at these lower temperatures. |
2378 |
|
2379 |
The $\tau_2^y$ results in the lower frame of figure |
2380 |
\ref{fig:t5peDynamics} show a much greater difference between the {\sc |
2381 |
sf} results and the Ewald results. At all temperatures shown, TIP5P-E |
2382 |
relaxes faster than experiment with the Ewald sum while tracking |
2383 |
experiment fairly well when using the {\sc sf} technique, independent |
2384 |
of the choice of damping constant. Their are several possible reasons |
2385 |
for this deviation between techniques. The Ewald results were taken |
2386 |
shorter (10ps) trajectories than the {\sc sf} results (25ps). A quick |
2387 |
calculation from a 10ps trajectory with {\sc sf} with an $\alpha$ of |
2388 |
0.2\AA$^-1$ at 25$^\circ$C showed a 0.4ps drop in $\tau_2^y$, placing |
2389 |
the result more in line with that obtained using the Ewald sum. These |
2390 |
results support this explanation; however, recomputing the results to |
2391 |
meet a poorer statistical standard is counter-productive. Assuming the |
2392 |
Ewald results are not the product of poor statistics, differences in |
2393 |
techniques to integrate the orientational motion could also play a |
2394 |
role. {\sc shake} is the most commonly used technique for |
2395 |
approximating rigid-body orientational motion,\cite{Ryckaert77} where |
2396 |
as in {\sc oopse}, we maintain and integrate the entire rotation |
2397 |
matrix using the {\sc dlm} method.\cite{Meineke05} Since {\sc shake} |
2398 |
is an iterative constraint technique, if the convergence tolerances |
2399 |
are raised for increased performance, error will accumulate in the |
2400 |
orientational motion. Finally, the Ewald results were calculated using |
2401 |
the $NVT$ ensemble, while the $NVE$ ensemble was used for {\sc sf} |
2402 |
calculations. The additional mode of motion due to the thermostat will |
2403 |
alter the dynamics, resulting in differences between $NVT$ and $NVE$ |
2404 |
results. These differences are increasingly noticeable as the |
2405 |
thermostat time constant decreases. |
2406 |
|
2407 |
\section{Damping of Point Multipoles}\label{sec:dampingMultipoles} |
2408 |
|
2409 |
As discussed above, the {\sc sp} and {\sc sf} methods operate by |
2410 |
neutralizing the cutoff sphere with charge-charge interaction shifting |
2411 |
and by damping the electrostatic interactions. Now we would like to |
2412 |
consider an extension of these techniques to include point multipole |
2413 |
interactions. How will the shifting and damping need to develop in |
2414 |
order to accommodate point multipoles? |
2415 |
|
2416 |
Of the two techniques, the least to vary is shifting. Shifting is |
2417 |
employed to neutralize the cutoff sphere; however, in a system |
2418 |
composed purely of point multipoles, the cutoff sphere is already |
2419 |
neutralized. This means that shifting is not necessary between point |
2420 |
multipoles. In a mixed system of monopoles and multipoles, the |
2421 |
undamped {\sc sf} potential needs only to shift the force terms of the |
2422 |
monopole (and use the monopole potential of equation (\ref{eq:SFPot})) |
2423 |
and smoothly cutoff the multipole interactions with a switching |
2424 |
function. The switching function is required in order to conserve |
2425 |
energy, because a discontinuity will exist at $R_\textrm{c}$ in the |
2426 |
absence of shifting terms. |
2427 |
|
2428 |
If we consider damping the {\sc sf} potential (Eq. (\ref{eq:DSFPot})), |
2429 |
then we need to incorporate the complimentary error function term into |
2430 |
the multipole potentials. The most direct way to do this is by |
2431 |
replacing $r^{-1}$ with erfc$(\alpha r)\cdot r^{-1}$ in the multipole |
2432 |
expansion.\cite{Hirschfelder67} In the multipole expansion, rather |
2433 |
than considering only the interactions between single point charges, |
2434 |
the electrostatic interactions is reformulated such that it describes |
2435 |
the interaction between charge distributions about central sites of |
2436 |
the respective sets of charges. This procedure is what leads to the |
2437 |
familiar charge-dipole, |
2438 |
\begin{equation} |
2439 |
V_\textrm{cd} = -q_i\frac{\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij}}{r^3_{ij}} |
2440 |
= -q_i\mu_j\frac{\cos\theta}{r^2_{ij}}, |
2441 |
\label{eq:chargeDipole} |
2442 |
\end{equation} |
2443 |
and dipole-dipole, |
2444 |
\begin{equation} |
2445 |
V_\textrm{dd} = 3\frac{(\boldsymbol{\mu}_i\cdot\mathbf{r}_{ij}) |
2446 |
(\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij})}{r^5_{ij}} - |
2447 |
\frac{\boldsymbol{\mu}_i\cdot\boldsymbol{\mu}_j}{r^3_{ij}}, |
2448 |
\label{eq:dipoleDipole} |
2449 |
\end{equation} |
2450 |
interaction potentials. |
2451 |
|
2452 |
Using the charge-dipole interaction as an example, if we insert |
2453 |
erfc$(\alpha r)\cdot r^{-1}$ in place of $r^{-1}$, a damped |
2454 |
charge-dipole results, |
2455 |
\begin{equation} |
2456 |
V_\textrm{Dcd} = -q_i\mu_j\frac{\cos\theta}{r^2_{ij}} c_1(r_{ij}), |
2457 |
\label{eq:dChargeDipole} |
2458 |
\end{equation} |
2459 |
where $c_1(r_{ij})$ is |
2460 |
\begin{equation} |
2461 |
c_1(r_{ij}) = \frac{2\alpha r_{ij}e^{-\alpha^2r^2_{ij}}}{\sqrt{\pi}} |
2462 |
+ \textrm{erfc}(\alpha r_{ij}). |
2463 |
\label{eq:c1Func} |
2464 |
\end{equation} |
2465 |
Thus, $c_1(r_{ij})$ is the resulting damping term that modifies the |
2466 |
standard charge-dipole potential (Eq. (\ref{eq:chargeDipole})). Note |
2467 |
that this damping term is dependent upon distance and not upon |
2468 |
orientation, and that it is acting on what was originally an |
2469 |
$r^{-3}_{ij}$ function. By writing the damped form in this manner, we |
2470 |
can collect the damping into one function and apply it to the original |
2471 |
potential when damping is desired. This works well for potentials that |
2472 |
have only one $r^{-n}$ term (where $n$ is an odd positive integer); |
2473 |
but in the case of the dipole-dipole potential, there is one part |
2474 |
dependent on $r^{-3}$ and another dependent on $r^{-5}$. In order to |
2475 |
properly damping this potential, each of these parts is dampened with |
2476 |
separate damping functions. We can determine the necessary damping |
2477 |
functions by continuing with the multipole expansion; however, it |
2478 |
quickly becomes more complex with ``two-center'' systems, like the |
2479 |
dipole-dipole potential, and is typically approached with a spherical |
2480 |
harmonic formalism.\cite{Hirschfelder67} A simpler method for |
2481 |
determining these functions arises from adopting the tensor formalism |
2482 |
for expressing the electrostatic interactions.\cite{Stone02} |
2483 |
|
2484 |
The tensor formalism for electrostatic interactions involves obtaining |
2485 |
the multipole interactions from successive gradients of the monopole |
2486 |
potential. Thus, tensors of rank one through three are |
2487 |
\begin{equation} |
2488 |
T = \frac{1}{4\pi\epsilon_0r_{ij}}, |
2489 |
\label{eq:tensorRank1} |
2490 |
\end{equation} |
2491 |
\begin{equation} |
2492 |
T_\alpha = \frac{1}{4\pi\epsilon_0}\nabla_\alpha \frac{1}{r_{ij}}, |
2493 |
\label{eq:tensorRank2} |
2494 |
\end{equation} |
2495 |
\begin{equation} |
2496 |
T_{\alpha\beta} = \frac{1}{4\pi\epsilon_0} |
2497 |
\nabla_\alpha\nabla_\beta \frac{1}{r_{ij}}, |
2498 |
\label{eq:tensorRank3} |
2499 |
\end{equation} |
2500 |
where the form of the first tensor gives the monopole-monopole |
2501 |
potential, the second gives the monopole-dipole potential, and the |
2502 |
third gives the monopole-quadrupole and dipole-dipole |
2503 |
potentials.\cite{Stone02} Since the force is $-\nabla V$, the forces |
2504 |
for each potential come from the next higher tensor. |
2505 |
|
2506 |
To obtain the damped electrostatic forms, we replace $r^{-1}$ with |
2507 |
erfc$(\alpha r)\cdot r^{-1}$. Equation \ref{eq:tensorRank2} generates |
2508 |
$c_1(r_{ij})$, just like the multipole expansion, while equation |
2509 |
\ref{eq:tensorRank3} generates $c_2(r_{ij})$, where |
2510 |
\begin{equation} |
2511 |
c_2(r_{ij}) = \frac{4\alpha^3r^3_{ij}e^{-\alpha^2r^2_{ij}}}{3\sqrt{\pi}} |
2512 |
+ \frac{2\alpha r_{ij}e^{-\alpha^2r^2_{ij}}}{\sqrt{\pi}} |
2513 |
+ \textrm{erfc}(\alpha r_{ij}). |
2514 |
\end{equation} |
2515 |
Note that $c_2(r_{ij})$ is equal to $c_1(r_{ij})$ plus an additional |
2516 |
term. Continuing with higher rank tensors, we can obtain the damping |
2517 |
functions for higher multipoles as well as the forces. Each subsequent |
2518 |
damping function includes one additional term, and we can simplify the |
2519 |
procedure for obtaining these terms by writing out the following |
2520 |
generating function, |
2521 |
\begin{equation} |
2522 |
c_n(r_{ij}) = \frac{2^n(\alpha r_{ij})^{2n-1}e^{-\alpha^2r^2_{ij}}} |
2523 |
{\sqrt{\pi}(2n-1)!!} + c_{n-1}(r_{ij}), |
2524 |
\label{eq:dampingGeneratingFunc} |
2525 |
\end{equation} |
2526 |
where, |
2527 |
\begin{equation} |
2528 |
m!! \equiv \left\{ \begin{array}{l@{\quad\quad}l} |
2529 |
m\cdot(m-2)\ldots 5\cdot3\cdot1 & m > 0\textrm{ odd} \\ |
2530 |
m\cdot(m-2)\ldots 6\cdot4\cdot2 & m > 0\textrm{ even} \\ |
2531 |
1 & m = -1\textrm{ or }0, |
2532 |
\end{array}\right. |
2533 |
\label{eq:doubleFactorial} |
2534 |
\end{equation} |
2535 |
and $c_0(r_{ij})$ is erfc$(\alpha r_{ij})$. This generating function |
2536 |
is similar in form to those obtained by researchers for the |
2537 |
application of the Ewald sum to |
2538 |
multipoles.\cite{Smith82,Smith98,Aguado03} |
2539 |
|
2540 |
Returning to the dipole-dipole example, the potential consists of a |
2541 |
portion dependent upon $r^{-5}$ and another dependent upon |
2542 |
$r^{-3}$. In the damped dipole-dipole potential, |
2543 |
\begin{equation} |
2544 |
V_\textrm{Ddd} = 3\frac{(\boldsymbol{\mu}_i\cdot\mathbf{r}_{ij}) |
2545 |
(\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij})}{r^5_{ij}} |
2546 |
c_2(r_{ij}) - |
2547 |
\frac{\boldsymbol{\mu}_i\cdot\boldsymbol{\mu}_j}{r^3_{ij}} |
2548 |
c_1(r_{ij}), |
2549 |
\label{eq:dampDipoleDipole} |
2550 |
\end{equation} |
2551 |
$c_2(r_{ij})$ and $c_1(r_{ij})$ respectively dampen these two |
2552 |
parts. The forces for the damped dipole-dipole interaction, |
2553 |
\begin{equation} |
2554 |
\begin{split} |
2555 |
F_\textrm{Ddd} = &15\frac{(\boldsymbol{\mu}_i\cdot\mathbf{r}_{ij}) |
2556 |
(\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij})\mathbf{r}_{ij}}{r^7_{ij}} |
2557 |
c_3(r_{ij})\\ &- |
2558 |
3\frac{\boldsymbol{\mu}_i\cdot\mathbf{r}_{ij}\cdot\hat{\boldsymbol{\mu}}_j + |
2559 |
\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij}\cdot\hat{\boldsymbol{\mu}}_i + |
2560 |
\boldsymbol{\mu}_i\cdot\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij}} |
2561 |
{r^5_{ij}} c_2(r_{ij}), |
2562 |
\end{split} |
2563 |
\label{eq:dampDipoleDipoleForces} |
2564 |
\end{equation} |
2565 |
rely on higher order damping functions because we perform another |
2566 |
gradient operation. In this manner, we can dampen higher order |
2567 |
multipolar interactions along with the monopole interactions, allowing |
2568 |
us to include multipoles in simulations involving damped electrostatic |
2569 |
interactions. |
2570 |
|
2571 |
|
2572 |
\section{Damping and Dielectric Constants}\label{sec:dampingDielectric} |
2573 |
|
2574 |
In section \ref{sec:t5peThermo}, we observed that the choice of |
2575 |
damping coefficient plays a major role in the calculated dielectric |
2576 |
constant. This is not too surprising given the results for damping |
2577 |
parameter influence on the long-time correlated motions of the NaCl |
2578 |
crystal in section \ref{sec:LongTimeDynamics}. The static dielectric |
2579 |
constant is calculated from the long-time fluctuations of the system's |
2580 |
accumulated dipole moment (Eq. (\ref{eq:staticDielectric})), so it is |
2581 |
going to be quite sensitive to the choice of damping parameter. We |
2582 |
would like to choose an optimal damping constant for any particular |
2583 |
cutoff radius choice that would properly capture the dielectric |
2584 |
behavior of the liquid. |
2585 |
|
2586 |
In order to find these optimal values, we mapped out the static |
2587 |
dielectric constant as a function of both the damping parameter and |
2588 |
cutoff radius for several different water models. To calculate the |
2589 |
static dielectric constant, we performed 5ns $NPT$ calculations at 9, |
2590 |
10, 11, and 12\AA cutoff radii, each with damping parameter values |
2591 |
ranging from 0 to 0.35\AA$^{-1}$ using the TIP5P-E, TIP4P-Ew, SPC/E, |
2592 |
and SSD/RF water models. TIP4P-Ew is a reparametrized version of the |
2593 |
four-point transferable intermolecular potential (TIP4P) for water |
2594 |
targeted for use with the Ewald summation.\cite{Horn04} SSD/RF is the |
2595 |
reaction field modified variant of the soft sticky dipole (SSD) model |
2596 |
for water, and this model is discussed in more detail in the next |
2597 |
chapter. One thing to note about it, electrostatic interactions are |
2598 |
handled via dipole-dipole interactions rather than charge-charge |
2599 |
interactions like the other three models. Damping of the dipole-dipole |
2600 |
interaction was handled as described in section |
2601 |
\ref{sec:dampingMultipoles}. |
2602 |
\begin{figure} |
2603 |
\centering |
2604 |
\includegraphics[width=3.5in]{./figures/dielectricMap.pdf} |
2605 |
\caption{The static dielectric constant for the A: TIP5P-E, B: TIP4P-Ew, |
2606 |
C: SPC/E, and D: SSD/RF water models as a function of cutoff radius |
2607 |
($R_\textrm{c}$) and damping coefficient ($\alpha$).} |
2608 |
\label{fig:dielectricMap} |
2609 |
\end{figure} |
2610 |
|
2611 |
The results of these calculations are displayed in figure |
2612 |
\ref{fig:dielectricMap} in the form of shaded contour plots. An |
2613 |
interesting aspect of all four contour plots is that the dielectric |
2614 |
constant is effectively linear with respect to $\alpha$ and |
2615 |
$R_\textrm{c}$ in the low to moderate damping regions. Another point |
2616 |
to note is that choosing $\alpha$ and $R_\textrm{c}$ identical to |
2617 |
those used in studies with the Ewald summation results in the same |
2618 |
calculated dielectric constant. As an example, in the paper outlining |
2619 |
the development of TIP5P-E, the real-space cutoff and Ewald |
2620 |
coefficient were tethered to the system size, and for a 512 molecule |
2621 |
system are approximately 12\AA and 0.25\AA$^{-1}$ |
2622 |
respectively.\cite{Rick04} These parameters resulted in a dielectric |
2623 |
constant of 92$\pm$14, while with {\sc sf} these parameters give a |
2624 |
dielectric constant of 90.8$\pm$0.9. Another example comes from the |
2625 |
TIP4P-Ew paper where $\alpha$ and $R_\textrm{c}$ were chosen to be |
2626 |
9.5\AA and 0.35\AA$^{-1}$, and these parameters resulted in a |
2627 |
$\epsilon_0$ equal to 63$\pm$1.\cite{Horn04} We did not perform |
2628 |
calculations with these exact parameters, but interpolating between |
2629 |
surrounding values gives a $\epsilon_0$ of 61$\pm$1. Seeing a |
2630 |
dependence of the dielectric constant on $\alpha$ and $R_\textrm{c}$ |
2631 |
with the {\sc sf} technique, it might be interesting to investigate |
2632 |
the dielectric dependence when using the Ewald summation. |
2633 |
|
2634 |
|
2635 |
|
2636 |
|
2637 |
\section{Conclusions}\label{sec:PairwiseConclusions} |
2638 |
|
2639 |
The above investigation of pairwise electrostatic summation techniques |
2640 |
shows that there are viable and computationally efficient alternatives |
2641 |
to the Ewald summation. These methods are derived from the damped and |
2642 |
cutoff-neutralized Coulombic sum originally proposed by Wolf |
2643 |
\textit{et al.}\cite{Wolf99} In particular, the {\sc sf} |
2644 |
method, reformulated above as equations (\ref{eq:DSFPot}) and |
2645 |
(\ref{eq:DSFForces}), shows a remarkable ability to reproduce the |
2646 |
energetic and dynamic characteristics exhibited by simulations |
2647 |
employing lattice summation techniques. The cumulative energy |
2648 |
difference results showed the undamped {\sc sf} and moderately damped |
2649 |
{\sc sp} methods produced results nearly identical to {\sc spme}. |
2650 |
Similarly for the dynamic features, the undamped or moderately damped |
2651 |
{\sc sf} and moderately damped {\sc sp} methods produce force and |
2652 |
torque vector magnitude and directions very similar to the expected |
2653 |
values. These results translate into long-time dynamic behavior |
2654 |
equivalent to that produced in simulations using {\sc spme}. |
2655 |
|
2656 |
As in all purely-pairwise cutoff methods, these methods are expected |
2657 |
to scale approximately {\it linearly} with system size, and they are |
2658 |
easily parallelizable. This should result in substantial reductions |
2659 |
in the computational cost of performing large simulations. |
2660 |
|
2661 |
Aside from the computational cost benefit, these techniques have |
2662 |
applicability in situations where the use of the Ewald sum can prove |
2663 |
problematic. Of greatest interest is their potential use in |
2664 |
interfacial systems, where the unmodified lattice sum techniques |
2665 |
artificially accentuate the periodicity of the system in an |
2666 |
undesirable manner. There have been alterations to the standard Ewald |
2667 |
techniques, via corrections and reformulations, to compensate for |
2668 |
these systems; but the pairwise techniques discussed here require no |
2669 |
modifications, making them natural tools to tackle these problems. |
2670 |
Additionally, this transferability gives them benefits over other |
2671 |
pairwise methods, like reaction field, because estimations of physical |
2672 |
properties (e.g. the dielectric constant) are unnecessary. |
2673 |
|
2674 |
If a researcher is using Monte Carlo simulations of large chemical |
2675 |
systems containing point charges, most structural features will be |
2676 |
accurately captured using the undamped {\sc sf} method or the {\sc sp} |
2677 |
method with an electrostatic damping of 0.2\AA$^{-1}$. These methods |
2678 |
would also be appropriate for molecular dynamics simulations where the |
2679 |
data of interest is either structural or short-time dynamical |
2680 |
quantities. For long-time dynamics and collective motions, the safest |
2681 |
pairwise method we have evaluated is the {\sc sf} method with an |
2682 |
electrostatic damping between 0.2 and 0.25\AA$^{-1}$. |
2683 |
|
2684 |
We are not suggesting that there is any flaw with the Ewald sum; in |
2685 |
fact, it is the standard by which these simple pairwise sums have been |
2686 |
judged. However, these results do suggest that in the typical |
2687 |
simulations performed today, the Ewald summation may no longer be |
2688 |
required to obtain the level of accuracy most researchers have come to |
2689 |
expect. |