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# Line 1 | Line 1
1 < \documentclass[12pt]{ndthesis}
1 > \documentclass[11pt]{ndthesis}
2  
3   % some packages for things like equations and graphics
4 + \usepackage[tbtags]{amsmath}
5   \usepackage{amsmath,bm}
6   \usepackage{amssymb}
7   \usepackage{mathrsfs}
8   \usepackage{tabularx}
9   \usepackage{graphicx}
10   \usepackage{booktabs}
11 + \usepackage{cite}
12 + \usepackage{enumitem}
13  
14   \begin{document}
15  
# Line 286 | Line 289 | properties obtained using the Ewald sum.
289   structural and dynamic properties of water compared the same
290   properties obtained using the Ewald sum.
291  
292 < \section{Simple Forms for Pairwise Electrostatics}
292 > \section{Simple Forms for Pairwise Electrostatics}\label{sec:PairwiseDerivation}
293  
294   The potentials proposed by Wolf \textit{et al.} and Zahn \textit{et
295   al.} are constructed using two different (and separable) computational
296   tricks:
297  
298 < \begin{enumerate}
298 > \begin{enumerate}[itemsep=0pt]
299   \item shifting through the use of image charges, and
300   \item damping the electrostatic interaction.
301   \end{enumerate}  
302 < Wolf \textit{et al.} treated the
303 < development of their summation method as a progressive application of
304 < these techniques,\cite{Wolf99} while Zahn \textit{et al.} founded
305 < their damped Coulomb modification (Eq. (\ref{eq:ZahnPot})) on the
306 < post-limit forces (Eq. (\ref{eq:WolfForces})) which were derived using
307 < both techniques.  It is possible, however, to separate these
308 < tricks and study their effects independently.
302 > Wolf \textit{et al.} treated the development of their summation method
303 > as a progressive application of these techniques,\cite{Wolf99} while
304 > Zahn \textit{et al.} founded their damped Coulomb modification
305 > (Eq. (\ref{eq:ZahnPot})) on the post-limit forces
306 > (Eq. (\ref{eq:WolfForces})) which were derived using both techniques.
307 > It is possible, however, to separate these tricks and study their
308 > effects independently.
309  
310   Starting with the original observation that the effective range of the
311   electrostatic interaction in condensed phases is considerably less
# Line 643 | Line 646 | crystals), so the systems studied were:
646   simulations (i.e. from liquids of neutral molecules to ionic
647   crystals), so the systems studied were:
648  
649 < \begin{enumerate}
649 > \begin{enumerate}[itemsep=0pt]
650   \item liquid water (SPC/E),\cite{Berendsen87}
651   \item crystalline water (Ice I$_\textrm{c}$ crystals of SPC/E),
652   \item NaCl crystals,
# Line 688 | Line 691 | from the reference method ({\sc spme}):
691   We compared the following alternative summation methods with results
692   from the reference method ({\sc spme}):
693  
694 < \begin{enumerate}
694 > \begin{enumerate}[itemsep=0pt]
695   \item {\sc sp} with damping parameters ($\alpha$) of 0.0, 0.1, 0.2,
696   and 0.3\AA$^{-1}$,
697   \item {\sc sf} with damping parameters ($\alpha$) of 0.0, 0.1, 0.2,
# Line 776 | Line 779 | limitations, primarily that it was developed for use i
779   the complementary error function is required).
780  
781   The reaction field results illustrates some of that method's
782 < limitations, primarily that it was developed for use in homogenous
782 > limitations, primarily that it was developed for use in homogeneous
783   systems; although it does provide results that are an improvement over
784   those from an unmodified cutoff.
785  
# Line 901 | Line 904 | angular behavior significantly for the {\sc sp} and mo
904   all do equivalently well at capturing the direction of both the force
905   and torque vectors.  Using the electrostatic damping improves the
906   angular behavior significantly for the {\sc sp} and moderately for the
907 < {\sc sf} methods.  Overdamping is detrimental to both methods.  Again
907 > {\sc sf} methods.  Over-damping is detrimental to both methods.  Again
908   it is important to recognize that the force vectors cover all
909   particles in all seven systems, while torque vectors are only
910   available for neutral molecular groups.  Damping is more beneficial to
911   charged bodies, and this observation is investigated further in
912 < section \ref{IndividualResults}.
912 > section \ref{sec:IndividualResults}.
913  
914   Although not discussed previously, group based cutoffs can be applied
915   to both the {\sc sp} and {\sc sf} methods.  The group-based cutoffs
# Line 932 | Line 935 | THE REFERENCE EWALD SUMMATION}
935  
936   \footnotesize
937   \begin{center}
938 < \begin{tabular}{@{} ccrrrrrrrr @{}} \\
938 > \begin{tabular}{@{} ccrrrrrrrr @{}}
939   \toprule
940   \toprule
938
941   & &\multicolumn{4}{c}{Shifted Potential} & \multicolumn{4}{c}{Shifted
942   Force} \\
943   \cmidrule(lr){3-6} \cmidrule(l){7-10} $R_\textrm{c}$ & Groups &
# Line 971 | Line 973 | However, at larger values of $\alpha$, it is possible
973   increases, something that is more obvious with group-based cutoffs.
974   The complimentary error function inserted into the potential weakens
975   the electrostatic interaction as the value of $\alpha$ is increased.
976 < However, at larger values of $\alpha$, it is possible to overdamp the
976 > However, at larger values of $\alpha$, it is possible to over-damp the
977   electrostatic interaction and to remove it completely.  Kast
978   \textit{et al.}  developed a method for choosing appropriate $\alpha$
979   values for these types of electrostatic summation methods by fitting
# Line 1008 | Line 1010 | abbreviations are as follows:
1010   investigated.  In all of the individual results table, the method
1011   abbreviations are as follows:
1012  
1013 < \begin{itemize}
1013 > \begin{itemize}[itemsep=0pt]
1014   \item PC = Pure Cutoff,
1015   \item SP = Shifted Potential,
1016   \item SF = Shifted Force,
# Line 1026 | Line 1028 | AND TORQUE VECTOR MAGNITUDES ({\it lower})}
1028  
1029   \footnotesize
1030   \begin{tabular}{@{} ccrrrrrr @{}}
1029 \\
1031   \toprule
1032   \toprule
1033   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1083 | Line 1084 | SYSTEM}
1084  
1085   \footnotesize
1086   \begin{tabular}{@{} ccrrrrrr @{}}
1086 \\
1087   \toprule
1088   \toprule
1089   & & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\
# Line 1121 | Line 1121 | with cutoff radii greater than 12\AA. Overdamping the
1121   agreement with {\sc spme} in both energetic and dynamic behavior when
1122   using the {\sc sf} method with and without damping. The {\sc sp}
1123   method does well with an $\alpha$ around 0.2\AA$^{-1}$, particularly
1124 < with cutoff radii greater than 12\AA. Overdamping the electrostatics
1124 > with cutoff radii greater than 12\AA. Over-damping the electrostatics
1125   reduces the agreement between both these methods and {\sc spme}.
1126  
1127   The pure cutoff ({\sc pc}) method performs poorly, again mirroring the
# Line 1154 | Line 1154 | ranges of interest.  When overdamping these methods, g
1154   no damping and only modest improvement for the recommended conditions
1155   ($\alpha = 0.2$\AA$^{-1}$ and $R_\textrm{c}~\geqslant~12$\AA).  The
1156   {\sc sf} method shows modest narrowing across all damping and cutoff
1157 < ranges of interest.  When overdamping these methods, group cutoffs and
1157 > ranges of interest.  When over-damping these methods, group cutoffs and
1158   the switching function do not improve the force and torque
1159   directionalities.
1160  
# Line 1180 | Line 1180 | middle}) AND TORQUE VECTOR MAGNITUDES ({\it lower})}
1180  
1181   \footnotesize
1182   \begin{tabular}{@{} ccrrrrrr @{}}
1183 \\
1183   \toprule
1184   \toprule
1185   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1236 | Line 1235 | OF THE FORCE AND TORQUE VECTORS IN THE ICE I$_\textrm{
1235  
1236   \footnotesize
1237   \begin{tabular}{@{} ccrrrrrr @{}}
1239 \\
1238   \toprule
1239   \toprule
1240   & & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque
# Line 1306 | Line 1304 | lower})}
1304  
1305   \footnotesize
1306   \begin{tabular}{@{} ccrrrrrr @{}}
1309 \\
1307   \toprule
1308   \toprule
1309   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1346 | Line 1343 | OF THE FORCE VECTORS IN THE MOLTEN SODIUM CHLORIDE SYS
1343  
1344   \footnotesize
1345   \begin{tabular}{@{} ccrrrrrr @{}}
1349 \\
1346   \toprule
1347   \toprule
1348   & & \multicolumn{3}{c}{Force $\sigma^2$} \\
# Line 1398 | Line 1394 | SYSTEM FOR $\Delta E$ VALUES ({\it upper}) AND FORCE V
1394  
1395   \footnotesize
1396   \begin{tabular}{@{} ccrrrrrr @{}}
1401 \\
1397   \toprule
1398   \toprule
1399   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1439 | Line 1434 | SYSTEM}
1434  
1435   \footnotesize
1436   \begin{tabular}{@{} ccrrrrrr @{}}
1442 \\
1437   \toprule
1438   \toprule
1439   & & \multicolumn{3}{c}{Force $\sigma^2$} \\
# Line 1498 | Line 1492 | SYSTEM FOR $\Delta E$ VALUES ({\it upper}), FORCE VECT
1492  
1493   \footnotesize
1494   \begin{tabular}{@{} ccrrrrrr @{}}
1501 \\
1495   \toprule
1496   \toprule
1497   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1555 | Line 1548 | CHLORIDE SOLUTION SYSTEM}
1548  
1549   \footnotesize
1550   \begin{tabular}{@{} ccrrrrrr @{}}
1558 \\
1551   \toprule
1552   \toprule
1553   & & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\
# Line 1619 | Line 1611 | SYSTEM FOR $\Delta E$ VALUES ({\it upper}), FORCE VECT
1611  
1612   \footnotesize
1613   \begin{tabular}{@{} ccrrrrrr @{}}
1622 \\
1614   \toprule
1615   \toprule
1616   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1676 | Line 1667 | SYSTEM}
1667  
1668   \footnotesize
1669   \begin{tabular}{@{} ccrrrrrr @{}}
1679 \\
1670   \toprule
1671   \toprule
1672   & & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\
# Line 1741 | Line 1731 | MAGNITUDES ({\it middle}) AND TORQUE VECTOR MAGNITUDES
1731  
1732   \footnotesize
1733   \begin{tabular}{@{} ccrrrrrr @{}}
1744 \\
1734   \toprule
1735   \toprule
1736   & & \multicolumn{2}{c}{9\AA} & \multicolumn{2}{c}{12\AA} & \multicolumn{2}{c}{15\AA}\\
# Line 1798 | Line 1787 | ARGON IN LIQUID WATER SYSTEM}  
1787  
1788   \footnotesize
1789   \begin{tabular}{@{} ccrrrrrr @{}}
1801 \\
1790   \toprule
1791   \toprule
1792   & & \multicolumn{3}{c}{Force $\sigma^2$} & \multicolumn{3}{c}{Torque $\sigma^2$} \\
# Line 1833 | Line 1821 | have aggrements similar to those observed in section
1821  
1822   This system does not appear to show any significant deviations from
1823   the previously observed results. The {\sc sp} and {\sc sf} methods
1824 < have aggrements similar to those observed in section
1824 > have agreements similar to those observed in section
1825   \ref{sec:WaterResults}. The only significant difference is the
1826   improvement in the configuration energy differences for the {\sc rf}
1827   method. This is surprising in that we are introducing an inhomogeneity
# Line 1953 | Line 1941 | with the power spectrum obtained using the Ewald sum.
1941   the NaCl crystal at 1000K.  The undamped shifted force ({\sc sf})
1942   method is off by less than 10 cm$^{-1}$, and increasing the
1943   electrostatic damping to 0.25\AA$^{-1}$ gives quantitative agreement
1944 < with the power spectrum obtained using the Ewald sum.  Overdamping can
1944 > with the power spectrum obtained using the Ewald sum.  Over-damping can
1945   result in underestimates of frequencies of the long-wavelength
1946   motions.}
1947   \label{fig:dampInc}
1948   \end{figure}
1949  
1950 < \section{Synopsis of the Pairwise Method Evaluation}\label{sec:PairwiseSynopsis}
1950 > \section{An Application: TIP5P-E Water}\label{sec:t5peApplied}
1951 >
1952 > The above sections focused on the energetics and dynamics of a variety
1953 > of systems when utilizing the {\sc sp} and {\sc sf} pairwise
1954 > techniques.  A unitary correlation with results obtained using the
1955 > Ewald summation should result in a successful reproduction of both the
1956 > static and dynamic properties of any selected system.  To test this,
1957 > we decided to calculate a series of properties for the TIP5P-E water
1958 > model when using the {\sc sf} technique.
1959 >
1960 > The TIP5P-E water model is a variant of Mahoney and Jorgensen's
1961 > five-point transferable intermolecular potential (TIP5P) model for
1962 > water.\cite{Mahoney00} TIP5P was developed to reproduce the density
1963 > maximum anomaly present in liquid water near 4$^\circ$C. As with many
1964 > previous point charge water models (such as ST2, TIP3P, TIP4P, SPC,
1965 > and SPC/E), TIP5P was parametrized using a simple cutoff with no
1966 > long-range electrostatic
1967 > correction.\cite{Stillinger74,Jorgensen83,Berendsen81,Berendsen87}
1968 > Without this correction, the pressure term on the central particle
1969 > from the surroundings is missing. Because they expand to compensate
1970 > for this added pressure term when this correction is included, systems
1971 > composed of these particles tend to underpredict the density of water
1972 > under standard conditions. When using any form of long-range
1973 > electrostatic correction, it has become common practice to develop or
1974 > utilize a reparametrized water model that corrects for this
1975 > effect.\cite{vanderSpoel98,Fennell04,Horn04} The TIP5P-E model follows
1976 > this practice and was optimized specifically for use with the Ewald
1977 > summation.\cite{Rick04} In his publication, Rick preserved the
1978 > geometry and point charge magnitudes in TIP5P and focused on altering
1979 > the Lennard-Jones parameters to correct the density at
1980 > 298K.\cite{Rick04} With the density corrected, he compared common
1981 > water properties for TIP5P-E using the Ewald sum with TIP5P using a
1982 > 9\AA\ cutoff.
1983 >
1984 > In the following sections, we compared these same water properties
1985 > calculated from TIP5P-E using the Ewald sum with TIP5P-E using the
1986 > {\sc sf} technique.  In the above evaluation of the pairwise
1987 > techniques, we observed some flexibility in the choice of parameters.
1988 > Because of this, the following comparisons include the {\sc sf}
1989 > technique with a 12\AA\ cutoff and an $\alpha$ = 0.0, 0.1, and
1990 > 0.2\AA$^{-1}$, as well as a 9\AA\ cutoff with an $\alpha$ =
1991 > 0.2\AA$^{-1}$.
1992 >
1993 > \subsection{Density}\label{sec:t5peDensity}
1994 >
1995 > As stated previously, the property that prompted the development of
1996 > TIP5P-E was the density at 1 atm.  The density depends upon the
1997 > internal pressure of the system in the $NPT$ ensemble, and the
1998 > calculation of the pressure includes a components from both the
1999 > kinetic energy and the virial. More specifically, the instantaneous
2000 > molecular pressure ($p(t)$) is given by
2001 > \begin{equation}
2002 > p(t) =  \frac{1}{\textrm{d}V}\sum_\mu
2003 >        \left[\frac{\mathbf{P}_{\mu}^2}{M_{\mu}}
2004 >        + \mathbf{R}_{\mu}\cdot\sum_i\mathbf{F}_{\mu i}\right],
2005 > \label{eq:MolecularPressure}
2006 > \end{equation}
2007 > where $V$ is the volume, $\mathbf{P}_{\mu}$ is the momentum of
2008 > molecule $\mu$, $\mathbf{R}_\mu$ is the position of the center of mass
2009 > ($M_\mu$) of molecule $\mu$, and $\mathbf{F}_{\mu i}$ is the force on
2010 > atom $i$ of molecule $\mu$.\cite{Melchionna93} The virial term (the
2011 > right term in the brackets of eq. \ref{eq:MolecularPressure}) is
2012 > directly dependent on the interatomic forces.  Since the {\sc sp}
2013 > method does not modify the forces (see
2014 > sec. \ref{sec:PairwiseDerivation}), the pressure using {\sc sp} will
2015 > be identical to that obtained without an electrostatic correction.
2016 > The {\sc sf} method does alter the virial component and, by way of the
2017 > modified pressures, should provide densities more in line with those
2018 > obtained using the Ewald summation.
2019 >
2020 > To compare densities, $NPT$ simulations were performed with the same
2021 > temperatures as those selected by Rick in his Ewald summation
2022 > simulations.\cite{Rick04} In order to improve statistics around the
2023 > density maximum, 3ns trajectories were accumulated at 0, 12.5, and
2024 > 25$^\circ$C, while 2ns trajectories were obtained at all other
2025 > temperatures. The average densities were calculated from the later
2026 > three-fourths of each trajectory. Similar to Mahoney and Jorgensen's
2027 > method for accumulating statistics, these sequences were spliced into
2028 > 200 segments to calculate the average density and standard deviation
2029 > at each temperature.\cite{Mahoney00}
2030 >
2031 > \begin{figure}
2032 > \includegraphics[width=\linewidth]{./figures/tip5peDensities.pdf}
2033 > \caption{Density versus temperature for the TIP5P-E water model when
2034 > using the Ewald summation (Ref. \cite{Rick04}) and the {\sc sf} method
2035 > with various parameters. The pressure term from the image-charge shell
2036 > is larger than that provided by the reciprocal-space portion of the
2037 > Ewald summation, leading to slightly lower densities. This effect is
2038 > more visible with the 9\AA\ cutoff, where the image charges exert a
2039 > greater force on the central particle. The error bars for the {\sc sf}
2040 > methods show plus or minus the standard deviation of the density
2041 > measurement at each temperature.}
2042 > \label{fig:t5peDensities}
2043 > \end{figure}
2044  
2045 + Figure \ref{fig:t5peDensities} shows the densities calculated for
2046 + TIP5P-E using differing electrostatic corrections overlaid on the
2047 + experimental values.\cite{CRC80} The densities when using the {\sc sf}
2048 + technique are close to, though typically lower than, those calculated
2049 + while using the Ewald summation. These slightly reduced densities
2050 + indicate that the pressure component from the image charges at
2051 + R$_\textrm{c}$ is larger than that exerted by the reciprocal-space
2052 + portion of the Ewald summation. Bringing the image charges closer to
2053 + the central particle by choosing a 9\AA\ R$_\textrm{c}$ (rather than
2054 + the preferred 12\AA\ R$_\textrm{c}$) increases the strength of their
2055 + interactions, resulting in a further reduction of the densities.
2056 +
2057 + Because the strength of the image charge interactions has a noticable
2058 + effect on the density, we would expect the use of electrostatic
2059 + damping to also play a role in these calculations. Larger values of
2060 + $\alpha$ weaken the pair-interactions; and since electrostatic damping
2061 + is distance-dependent, force components from the image charges will be
2062 + reduced more than those from particles close the the central
2063 + charge. This effect is visible in figure \ref{fig:t5peDensities} with
2064 + the damped {\sc sf} sums showing slightly higher densities; however,
2065 + it is apparent that the choice of cutoff radius plays a much more
2066 + important role in the resulting densities.
2067 +
2068 + As a final note, all of the above density calculations were performed
2069 + with systems of 512 water molecules. Rick observed a system sized
2070 + dependence of the computed densities when using the Ewald summation,
2071 + most likely due to his tying of the convergence parameter to the box
2072 + dimensions.\cite{Rick04} For systems of 256 water molecules, the
2073 + calculated densities were on average 0.002 to 0.003 g/cm$^3$ lower. A
2074 + system size of 256 molecules would force the use of a shorter
2075 + R$_\textrm{c}$ when using the {\sc sf} technique, and this would also
2076 + lower the densities. Moving to larger systems, as long as the
2077 + R$_\textrm{c}$ remains at a fixed value, we would expect the densities
2078 + to remain constant.
2079 +
2080 + \subsection{Liquid Structure}\label{sec:t5peLiqStructure}
2081 +
2082 + A common function considered when developing and comparing water
2083 + models is the oxygen-oxygen radial distribution function
2084 + ($g_\textrm{OO}(r)$). The $g_\textrm{OO}(r)$ is the probability of
2085 + finding a pair of oxygen atoms some distance ($r$) apart relative to a
2086 + random distribution at the same density.\cite{Allen87} It is
2087 + calculated via
2088 + \begin{equation}
2089 + g_\textrm{OO}(r) = \frac{V}{N^2}\left\langle\sum_i\sum_{j\ne i}
2090 +        \delta(\mathbf{r}-\mathbf{r}_{ij})\right\rangle,
2091 + \label{eq:GOOofR}
2092 + \end{equation}
2093 + where the double sum is over all $i$ and $j$ pairs of $N$ oxygen
2094 + atoms. The $g_\textrm{OO}(r)$ can be directly compared to X-ray or
2095 + neutron scattering experiments through the oxygen-oxygen structure
2096 + factor ($S_\textrm{OO}(k)$) by the following relationship:
2097 + \begin{equation}
2098 + S_\textrm{OO}(k) = 1 + 4\pi\rho
2099 +        \int_0^\infty r^2\frac{\sin kr}{kr}g_\textrm{OO}(r)\textrm{d}r.
2100 + \label{eq:SOOofK}
2101 + \end{equation}
2102 + Thus, $S_\textrm{OO}(k)$ is related to the Fourier-Laplace transform
2103 + of $g_\textrm{OO}(r)$.
2104 +
2105 + The expermentally determined $g_\textrm{OO}(r)$ for liquid water has
2106 + been compared in great detail with the various common water models,
2107 + and TIP5P was found to be in better agreement than other rigid,
2108 + non-polarizable models.\cite{Sorenson00} This excellent agreement with
2109 + experiment was maintained when Rick developed TIP5P-E.\cite{Rick04} To
2110 + check whether the choice of using the Ewald summation or the {\sc sf}
2111 + technique alters the liquid structure, the $g_\textrm{OO}(r)$s at 298K
2112 + and 1atm were determined for the systems compared in the previous
2113 + section.
2114 +
2115 + \begin{figure}
2116 + \includegraphics[width=\linewidth]{./figures/tip5peGofR.pdf}
2117 + \caption{The $g_\textrm{OO}(r)$s calculated for TIP5P-E at 298K and
2118 + 1atm while using the Ewald summation (Ref. \cite{Rick04}) and the {\sc
2119 + sf} technique with varying parameters. Even with the reduced densities
2120 + using the {\sc sf} technique, the $g_\textrm{OO}(r)$s are essentially
2121 + identical.}
2122 + \label{fig:t5peGofRs}
2123 + \end{figure}
2124 +
2125 + The $g_\textrm{OO}(r)$s calculated for TIP5P-E while using the {\sc
2126 + sf} technique with a various parameters are overlaid on the
2127 + $g_\textrm{OO}(r)$ while using the Ewald summation. The differences in
2128 + density do not appear to have any effect on the liquid structure as
2129 + the $g_\textrm{OO}(r)$s are indistinquishable. These results indicate
2130 + that the $g_\textrm{OO}(r)$ is insensitive to the choice of
2131 + electrostatic correction.
2132 +
2133 + \subsection{Thermodynamic Properties}\label{sec:t5peThermo}
2134 +
2135 + In addition to the density, there are a variety of thermodynamic
2136 + quantities that can be calculated for water and compared directly to
2137 + experimental values. Some of these additional quatities include the
2138 + latent heat of vaporization ($\Delta H_\textrm{vap}$), the constant
2139 + pressure heat capacity ($C_p$), the isothermal compressibility
2140 + ($\kappa_T$), the thermal expansivity ($\alpha_p$), and the static
2141 + dielectric constant ($\epsilon$). All of these properties were
2142 + calculated for TIP5P-E with the Ewald summation, so they provide a
2143 + good set for comparisons involving the {\sc sf} technique.
2144 +
2145 + The $\Delta H_\textrm{vap}$ is the enthalpy change required to
2146 + transform one mol of substance from the liquid phase to the gas
2147 + phase.\cite{Berry00} In molecular simulations, this quantity can be
2148 + determined via
2149 + \begin{equation}
2150 + \begin{split}
2151 + \Delta H_\textrm{vap} &= H_\textrm{gas} - H_\textrm{liq.} \\
2152 +                      &= E_\textrm{gas} - E_\textrm{liq.}
2153 +                        + p(V_\textrm{gas} - V_\textrm{liq.}) \\
2154 +                      &\approx -\frac{\langle U_\textrm{liq.}\rangle}{N}+ RT,
2155 + \end{split}
2156 + \label{eq:DeltaHVap}
2157 + \end{equation}
2158 + where $E$ is the total energy, $U$ is the potential energy, $p$ is the
2159 + pressure, $V$ is the volume, $N$ is the number of molecules, $R$ is
2160 + the gas constant, and $T$ is the temperature.\cite{Jorgensen98b} As
2161 + seen in the last line of equation \ref{eq:DeltaHVap}, we can
2162 + approximate $\Delta H_\textrm{vap}$ by using the ideal gas for the gas
2163 + state. This allows us to cancel the kinetic energy terms, leaving only
2164 + the $U_\textrm{liq.}$ term. Additionally, the $pV$ term for the gas is
2165 + several orders of magnitude larger than that of the liquid, so we can
2166 + neglect the liquid $pV$ term.
2167 +
2168 + The remaining thermodynamic properties can all be calculated from
2169 + fluctuations of the enthalpy, volume, and system dipole
2170 + moment.\cite{Allen87} $C_p$ can be calculated from fluctuations in the
2171 + enthalpy in constant pressure simulations via
2172 + \begin{equation}
2173 + \begin{split}
2174 + C_p     = \left(\frac{\partial H}{\partial T}\right)_{N,p}
2175 +        = \frac{(\langle H^2\rangle - \langle H\rangle^2)}{Nk_BT^2},
2176 + \end{split}
2177 + \label{eq:Cp}
2178 + \end{equation}
2179 + where $k_B$ is Boltzmann's constant.  $\kappa_T$ can be calculated via
2180 + \begin{equation}
2181 + \begin{split}
2182 + \kappa_T = \frac{1}{V}\left(\frac{\partial V}{\partial p}\right)_{N,T}
2183 +         = \frac{(\langle V^2\rangle_{N,P,T} - \langle V\rangle^2_{N,P,T})}
2184 +                {k_BT\langle V\rangle_{N,P,T}},
2185 + \end{split}
2186 + \label{eq:kappa}
2187 + \end{equation}
2188 + and $\alpha_p$ can be calculated via
2189 + \begin{equation}
2190 + \begin{split}
2191 + \alpha_p        = \frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_{N,P}
2192 +                = \frac{(\langle VH\rangle_{N,P,T}
2193 +                        - \langle V\rangle_{N,P,T}\langle H\rangle_{N,P,T})}
2194 +                        {k_BT^2\langle V\rangle_{N,P,T}}.
2195 + \end{split}
2196 + \label{eq:alpha}
2197 + \end{equation}
2198 + Using the Ewald sum under tin-foil boundary conditions, $\epsilon$ can
2199 + be calculated for systems of non-polarizable substances via
2200 + \begin{equation}
2201 + \epsilon = 1 + \frac{\langle M^2\rangle}{3\epsilon_0k_\textrm{B}TV},
2202 + \label{eq:staticDielectric}
2203 + \end{equation}
2204 + where $\epsilon_0$ is the permittivity of free space and $\langle
2205 + M^2\rangle$ is the fluctuation of the system dipole
2206 + moment.\cite{Allen87} The numerator in the fractional term in equation
2207 + \ref{eq:staticDielectric} is the fluctuation of the simulation-box
2208 + dipole moment, identical to the quantity calculated in the
2209 + finite-system Kirkwood $g$ factor ($G_k$):
2210 + \begin{equation}
2211 + G_k = \frac{\langle M^2\rangle}{N\mu^2},
2212 + \label{eq:KirkwoodFactor}
2213 + \end{equation}
2214 + where $\mu$ is the dipole moment of a single molecule of the
2215 + homogeneous system.\cite{Neumann83,Neumann84,Neumann85} The
2216 + fluctuation term in both equation \ref{eq:staticDielectric} and
2217 + \ref{eq:KirkwoodFactor} is calculated as follows,
2218 + \begin{equation}
2219 + \begin{split}
2220 + \langle M^2\rangle &= \langle\bm{M}\cdot\bm{M}\rangle
2221 +                        - \langle\bm{M}\rangle\cdot\langle\bm{M}\rangle \\
2222 +                   &= \langle M_x^2+M_y^2+M_z^2\rangle
2223 +                        - (\langle M_x\rangle^2 + \langle M_x\rangle^2
2224 +                                + \langle M_x\rangle^2).        
2225 + \end{split}
2226 + \label{eq:fluctBoxDipole}
2227 + \end{equation}
2228 + This fluctuation term can be accumulated during the simulation;
2229 + however, it converges rather slowly, thus requiring multi-nanosecond
2230 + simulation times.\cite{Horn04} In the case of tin-foil boundary
2231 + conditions, the dielectric/surface term of equation \ref{eq:EwaldSum}
2232 + is equal to zero. Since the {\sc sf} method also lacks this
2233 + dielectric/surface term, equation \ref{eq:staticDielectric} is still
2234 + valid for determining static dielectric constants.
2235 +
2236 + All of the above properties were calculated from the same trajectories
2237 + used to determine the densities in section \ref{sec:t5peDensity}
2238 + except for the static dielectric constants. The $\epsilon$ values were
2239 + accumulated from 2ns $NVE$ ensemble trajectories with system densities
2240 + fixed at the average values from the $NPT$ simulations at each of the
2241 + temperatures. The resulting values are displayed in figure
2242 + \ref{fig:t5peThermo}.
2243 + \begin{figure}
2244 + \centering
2245 + \includegraphics[width=5.5in]{./figures/t5peThermo.pdf}
2246 + \caption{Thermodynamic properties for TIP5P-E using the Ewald summation
2247 + and the {\sc sf} techniques along with the experimental values. Units
2248 + for the properties are kcal mol$^{-1}$ for $\Delta H_\textrm{vap}$,
2249 + cal mol$^{-1}$ K$^{-1}$ for $C_p$, 10$^6$ atm$^{-1}$ for $\kappa_T$,
2250 + and 10$^5$ K$^{-1}$ for $\alpha_p$. Ewald summation results are from
2251 + reference \cite{Rick04}. Experimental values for $\Delta
2252 + H_\textrm{vap}$, $\kappa_T$, and $\alpha_p$ are from reference
2253 + \cite{Kell75}. Experimental values for $C_p$ are from reference
2254 + \cite{Wagner02}. Experimental values for $\epsilon$ are from reference
2255 + \cite{Malmberg56}.}
2256 + \label{fig:t5peThermo}
2257 + \end{figure}
2258 +
2259 + As observed for the density in section \ref{sec:t5peDensity}, the
2260 + property trends with temperature seen when using the Ewald summation
2261 + are reproduced with the {\sc sf} technique. Differences include the
2262 + calculated values of $\Delta H_\textrm{vap}$ underpredicting the Ewald
2263 + values. This is to be expected due to the direct weakening of the
2264 + electrostatic interaction through forced neutralization in {\sc
2265 + sf}. This results in an increase of the intermolecular potential
2266 + producing lower values from equation \ref{eq:DeltaHVap}. The slopes of
2267 + these values with temperature are similar to that seen using the Ewald
2268 + summation; however, they are both steeper than the experimental trend,
2269 + indirectly resulting in the inflated $C_p$ values at all temperatures.
2270 +
2271 + Above the supercooled regim\'{e}, $C_p$, $\kappa_T$, and $\alpha_p$
2272 + values all overlap within error. As indicated for the $\Delta
2273 + H_\textrm{vap}$ and $C_p$ results discussed in the previous paragraph,
2274 + the deviations between experiment and simulation in this region are
2275 + not the fault of the electrostatic summation methods but are due to
2276 + the TIP5P class model itself. Like most rigid, non-polarizable,
2277 + point-charge water models, the density decreases with temperature at a
2278 + much faster rate than experiment (see figure
2279 + \ref{fig:t5peDensities}). The reduced density leads to the inflated
2280 + compressibility and expansivity values at higher temperatures seen
2281 + here in figure \ref{fig:t5peThermo}. Incorporation of polarizability
2282 + and many-body effects are required in order for simulation to overcome
2283 + these differences with experiment.\cite{Laasonen93,Donchev06}
2284 +
2285 + At temperatures below the freezing point for experimental water, the
2286 + differences between {\sc sf} and the Ewald summation results are more
2287 + apparent. The larger $C_p$ and lower $\alpha_p$ values in this region
2288 + indicate a more pronounced transition in the supercooled regim\'{e},
2289 + particularly in the case of {\sc sf} without damping. This points to
2290 + the onset of a more frustrated or glassy behavior for TIP5P-E at
2291 + temperatures below 250K in these simulations. Because the systems are
2292 + locked in different regions of phase-space, comparisons between
2293 + properties at these temperatures are not exactly fair. This
2294 + observation is explored in more detail in section
2295 + \ref{sec:t5peDynamics}.
2296 +
2297 + The final thermodynamic property displayed in figure
2298 + \ref{fig:t5peThermo}, $\epsilon$, shows the greatest discrepancy
2299 + between the Ewald summation and the {\sc sf} technique (and experiment
2300 + for that matter). It is known that the dielectric constant is
2301 + dependent upon and quite sensitive to the imposed boundary
2302 + conditions.\cite{Neumann80,Neumann83} This is readily apparent in the
2303 + converged $\epsilon$ values accumulated for the {\sc sf}
2304 + simulations. Lack of a damping function results in dielectric
2305 + constants significantly smaller than that obtained using the Ewald
2306 + sum. Increasing the damping coefficient to 0.2\AA$^{-1}$ improves the
2307 + agreement considerably. It should be noted that the choice of the
2308 + ``Ewald coefficient'' value also has a significant effect on the
2309 + calculated value when using the Ewald summation. In the simulations of
2310 + TIP5P-E with the Ewald sum, this screening parameter was tethered to
2311 + the simulation box size (as was the $R_\textrm{c}$).\cite{Rick04}
2312 + Systems with larger screening parameters reported larger dielectric
2313 + constant values, the same behavior we see here with {\sc sf}. In
2314 + section \ref{sec:dampingDielectric}, this connection is further
2315 + explored as optimal damping coefficients are determined for {\sc
2316 + sf} for capturing the dielectric behavior.
2317 +
2318 + \subsection{Dynamic Properties}\label{sec:t5peDynamics}
2319 +
2320 + To look at the dynamic properties of TIP5P-E when using the {\sc sf}
2321 + method, 200ps $NVE$ simulations were performed for each temperature at
2322 + the average density reported by the $NPT$ simulations. The
2323 + self-diffusion constants ($D$) were calculated with the Einstein
2324 + relation using the mean square displacement (MSD),
2325 + \begin{equation}
2326 + D = \frac{\langle\left|\mathbf{r}_i(t)-\mathbf{r}_i(0)\right|^2\rangle}{6t},
2327 + \label{eq:MSD}
2328 + \end{equation}
2329 + where $t$ is time, and $\mathbf{r}_i$ is the position of particle
2330 + $i$.\cite{Allen87} Figure \ref{fig:ExampleMSD} shows an example MSD
2331 + plot. As labeled in the figure, MSD plots consist of three distinct
2332 + regions:
2333 +
2334 + \begin{enumerate}[itemsep=0pt]
2335 + \item parabolic short-time ballistic motion,
2336 + \item linear diffusive regime, and
2337 + \item poor statistic region at long-time.
2338 + \end{enumerate}
2339 + The slope from the linear region (region 2) is used to calculate $D$.
2340 + \begin{figure}
2341 + \centering
2342 + \includegraphics[width=3.5in]{./figures/ExampleMSD.pdf}
2343 + \caption{Example plot of mean square displacement verses time. The
2344 + left red region is the ballistic motion regime, the middle green
2345 + region is the linear diffusive regime, and the right blue region is
2346 + the region with poor statistics.}
2347 + \label{fig:ExampleMSD}
2348 + \end{figure}
2349 +
2350 + \begin{figure}
2351 + \centering
2352 + \includegraphics[width=3.5in]{./figures/waterFrame.pdf}
2353 + \caption{Body-fixed coordinate frame for a water molecule. The
2354 + respective molecular principle axes point in the direction of the
2355 + labeled frame axes.}
2356 + \label{fig:waterFrame}
2357 + \end{figure}
2358 + In addition to translational diffusion, reorientational time constants
2359 + were calculated for comparisons with the Ewald simulations and with
2360 + experiments. These values were determined from 25ps $NVE$ trajectories
2361 + through calculation of the orientational time correlation function,
2362 + \begin{equation}
2363 + C_l^\alpha(t) = \left\langle P_l\left[\hat{\mathbf{u}}_i^\alpha(t)
2364 +                \cdot\hat{\mathbf{u}}_i^\alpha(0)\right]\right\rangle,
2365 + \label{eq:OrientCorr}
2366 + \end{equation}
2367 + where $P_l$ is the Legendre polynomial of order $l$ and
2368 + $\hat{\mathbf{u}}_i^\alpha$ is the unit vector of molecule $i$ along
2369 + principle axis $\alpha$. The principle axis frame for these water
2370 + molecules is shown in figure \ref{fig:waterFrame}. As an example,
2371 + $C_l^y$ is calculated from the time evolution of the unit vector
2372 + connecting the two hydrogen atoms.
2373 +
2374 + \begin{figure}
2375 + \centering
2376 + \includegraphics[width=3.5in]{./figures/ExampleOrientCorr.pdf}
2377 + \caption{Example plots of the orientational autocorrelation functions
2378 + for the first and second Legendre polynomials. These curves show the
2379 + time decay of the unit vector along the $y$ principle axis.}
2380 + \label{fig:OrientCorr}
2381 + \end{figure}
2382 + From the orientation autocorrelation functions, we can obtain time
2383 + constants for rotational relaxation. Figure \ref{fig:OrientCorr} shows
2384 + some example plots of orientational autocorrelation functions for the
2385 + first and second Legendre polynomials. The relatively short time
2386 + portions (between 1 and 3ps for water) of these curves can be fit to
2387 + an exponential decay to obtain these constants, and they are directly
2388 + comparable to water orientational relaxation times from nuclear
2389 + magnetic resonance (NMR). The relaxation constant obtained from
2390 + $C_2^y(t)$ is of particular interest because it is about the principle
2391 + axis with the minimum moment of inertia and should thereby dominate
2392 + the orientational relaxation of the molecule.\cite{Impey82} This means
2393 + that $C_2^y(t)$ should provide the best comparison to the NMR
2394 + relaxation data.
2395 +
2396 + \begin{figure}
2397 + \centering
2398 + \includegraphics[width=5.5in]{./figures/t5peDynamics.pdf}
2399 + \caption{Diffusion constants ({\it upper}) and reorientational time
2400 + constants ({\it lower}) for TIP5P-E using the Ewald sum and {\sc sf}
2401 + technique compared with experiment. Data at temperatures less that
2402 + 0$^\circ$C were not included in the $\tau_2^y$ plot to allow for
2403 + easier comparisons in the more relavent temperature regime.}
2404 + \label{fig:t5peDynamics}
2405 + \end{figure}
2406 + Results for the diffusion constants and reorientational time constants
2407 + are shown in figure \ref{fig:t5peDynamics}. From this figure, it is
2408 + apparent that the trends for both $D$ and $\tau_2^y$ of TIP5P-E using
2409 + the Ewald sum are reproduced with the {\sc sf} techinque. The enhanced
2410 + diffusion at high temperatures are again the product of the lower
2411 + densities in comparison with experiment and do not provide any special
2412 + insight into differences between the electrostatic summation
2413 + techniques. With the undamped {\sc sf} technique, TIP5P-E tends to
2414 + diffuse a little faster than with the Ewald sum; however, use of light
2415 + to moderate damping results in indistiguishable $D$ values. Though not
2416 + apparent in this figure, {\sc sf} values at the lowest temperature are
2417 + approximately an order of magnitude lower than with Ewald. These
2418 + values support the observation from section \ref{sec:t5peThermo} that
2419 + there appeared to be a change to a more glassy-like phase with the
2420 + {\sc sf} technique at these lower temperatures.
2421 +
2422 + The $\tau_2^y$ results in the lower frame of figure
2423 + \ref{fig:t5peDynamics} show a much greater difference between the {\sc
2424 + sf} results and the Ewald results. At all temperatures shown, TIP5P-E
2425 + relaxes faster than experiment with the Ewald sum while tracking
2426 + experiment fairly well when using the {\sc sf} technique, independent
2427 + of the choice of damping constant. Their are several possible reasons
2428 + for this deviation between techniques. The Ewald results were taken
2429 + shorter (10ps) trajectories than the {\sc sf} results (25ps). A quick
2430 + calculation from a 10ps trajectory with {\sc sf} with an $\alpha$ of
2431 + 0.2\AA$^-1$ at 25$^\circ$C showed a 0.4ps drop in $\tau_2^y$, placing
2432 + the result more in line with that obtained using the Ewald sum. These
2433 + results support this explanation; however, recomputing the results to
2434 + meet a poorer statistical standard is counter-productive. Assuming the
2435 + Ewald results are not the product of poor statistics, differences in
2436 + techniques to integrate the orientational motion could also play a
2437 + role. {\sc shake} is the most commonly used technique for
2438 + approximating rigid-body orientational motion,\cite{Ryckaert77} where
2439 + as in {\sc oopse}, we maintain and integrate the entire rotation
2440 + matrix using the {\sc dlm} method.\cite{Meineke05} Since {\sc shake}
2441 + is an iterative constraint technique, if the convergence tolerances
2442 + are raised for increased performance, error will accumulate in the
2443 + orientational motion. Finally, the Ewald results were calculated using
2444 + the $NVT$ ensemble, while the $NVE$ ensemble was used for {\sc sf}
2445 + calculations. The additional mode of motion due to the thermostat will
2446 + alter the dynamics, resulting in differences between $NVT$ and $NVE$
2447 + results. These differences are increasingly noticable as the
2448 + thermostat time constant decreases.
2449 +
2450 + \section{Damping of Point Multipoles}\label{sec:dampingMultipoles}
2451 +
2452 +
2453 +
2454 + \section{Damping and Dielectric Constants}\label{sec:dampingDielectric}
2455 +
2456 + \section{Conclusions}\label{sec:PairwiseConclusions}
2457 +
2458   The above investigation of pairwise electrostatic summation techniques
2459   shows that there are viable and computationally efficient alternatives
2460   to the Ewald summation.  These methods are derived from the damped and
# Line 2013 | Line 2507 | expect.
2507   required to obtain the level of accuracy most researchers have come to
2508   expect.
2509  
2016 \section{An Application: TIP5P-E Water}
2017
2018
2510   \chapter{\label{chap:water}SIMPLE MODELS FOR WATER}
2511  
2512   \chapter{\label{chap:ice}PHASE BEHAVIOR OF WATER IN COMPUTER SIMULATIONS}

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