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# Line 35 | Line 35 | preprint,
35   %\linenumbers\relax % Commence numbering lines
36   \usepackage{amsmath}
37   \usepackage{times}
38 < \usepackage{mathptm}
38 > \usepackage{mathptmx}
39   \usepackage{tabularx}
40   \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
41   \usepackage{url}
# Line 70 | Line 70 | of Notre Dame, Notre Dame, IN 46556}
70    We have tested the real-space shifted potential (SP),
71    gradient-shifted force (GSF), and Taylor-shifted force (TSF) methods
72    for multipoles that were developed in the first paper in this series
73 <  against a reference method. The tests were carried out in a variety
74 <  of condensed-phase environments which were designed to test all
75 <  levels of the multipole-multipole interactions.  Comparisons of the
76 <  energy differences between configurations, molecular forces, and
77 <  torques were used to analyze how well the real-space models perform
78 <  relative to the more computationally expensive Ewald sum.  We have
79 <  also investigated the energy conservation properties of the new
80 <  methods in molecular dynamics simulations using all of these
81 <  methods. The SP method shows excellent agreement with
82 <  configurational energy differences, forces, and torques, and would
83 <  be suitable for use in Monte Carlo calculations.  Of the two new
84 <  shifted-force methods, the GSF approach shows the best agreement
85 <  with Ewald-derived energies, forces, and torques and exhibits energy
86 <  conservation properties that make it an excellent choice for
87 <  efficiently computing electrostatic interactions in molecular
88 <  dynamics simulations.
73 >  against the multipolar Ewald sum as a reference method. The tests
74 >  were carried out in a variety of condensed-phase environments which
75 >  were designed to test all levels of the multipole-multipole
76 >  interactions.  Comparisons of the energy differences between
77 >  configurations, molecular forces, and torques were used to analyze
78 >  how well the real-space models perform relative to the more
79 >  computationally expensive Ewald treatment.  We have also investigated the
80 >  energy conservation properties of the new methods in molecular
81 >  dynamics simulations using all of these methods. The SP method shows
82 >  excellent agreement with configurational energy differences, forces,
83 >  and torques, and would be suitable for use in Monte Carlo
84 >  calculations.  Of the two new shifted-force methods, the GSF
85 >  approach shows the best agreement with Ewald-derived energies,
86 >  forces, and torques and exhibits energy conservation properties that
87 >  make it an excellent choice for efficiently computing electrostatic
88 >  interactions in molecular dynamics simulations.
89   \end{abstract}
90  
91   %\pacs{Valid PACS appear here}% PACS, the Physics and Astronomy
92                               % Classification Scheme.
93 < \keywords{Electrostatics, Multipoles, Real-space}
93 > %\keywords{Electrostatics, Multipoles, Real-space}
94  
95   \maketitle
96  
# Line 120 | Line 120 | To simulate interfacial systems, Parry’s extension o
120   method may require modification to compute interactions for
121   interfacial molecular systems such as membranes and liquid-vapor
122   interfaces.\cite{Parry:1975if,Parry:1976fq,Clarke77,Perram79,Rhee:1989kl}
123 < To simulate interfacial systems, Parry’s extension of the 3D Ewald sum
123 > To simulate interfacial systems, Parry's extension of the 3D Ewald sum
124   is appropriate for slab geometries.\cite{Parry:1975if} The inherent
125 < periodicity in the Ewald’s method can also be problematic for
126 < interfacial molecular systems.\cite{Fennell:2006lq} Modified Ewald
127 < methods that were developed to handle two-dimensional (2D)
128 < electrostatic interactions in interfacial systems have not had similar
129 < particle-mesh treatments.\cite{Parry:1975if, Parry:1976fq, Clarke77,
130 <  Perram79,Rhee:1989kl,Spohr:1997sf,Yeh:1999oq}
125 > periodicity in the Ewald method can also be problematic for molecular
126 > interfaces.\cite{Fennell:2006lq} Modified Ewald methods that were
127 > developed to handle two-dimensional (2D) electrostatic interactions in
128 > interfacial systems have not seen similar particle-mesh
129 > treatments,\cite{Parry:1975if, Parry:1976fq, Clarke77,
130 >  Perram79,Rhee:1989kl,Spohr:1997sf,Yeh:1999oq} and still scale poorly
131 > with system size.
132  
133   \subsection{Real-space methods}
134   Wolf \textit{et al.}\cite{Wolf:1999dn} proposed a real space $O(N)$
135   method for calculating electrostatic interactions between point
136   charges. They argued that the effective Coulomb interaction in
137 < condensed systems is actually short ranged.\cite{Wolf92,Wolf95}.  For
138 < an ordered lattice (e.g. when computing the Madelung constant of an
139 < ionic solid), the material can be considered as a set of ions
137 > condensed phase systems is actually short ranged.\cite{Wolf92,Wolf95}
138 > For an ordered lattice (e.g., when computing the Madelung constant of
139 > an ionic solid), the material can be considered as a set of ions
140   interacting with neutral dipolar or quadrupolar ``molecules'' giving
141   an effective distance dependence for the electrostatic interactions of
142 < $r^{-5}$ (see figure \ref{fig:NaCl}.  For this reason, careful
143 < applications of Wolf's method are able to obtain accurate estimates of
144 < Madelung constants using relatively short cutoff radii.  Recently,
145 < Fukuda used neutralization of the higher order moments for the
146 < calculation of the electrostatic interaction of the point charges
147 < system.\cite{Fukuda:2013sf}
142 > $r^{-5}$ (see figure \ref{fig:schematic}).  For this reason, careful
143 > application of Wolf's method can obtain accurate estimates of Madelung
144 > constants using relatively short cutoff radii.  Recently, Fukuda used
145 > neutralization of the higher order moments for calculation of the
146 > electrostatic interactions in point charge
147 > systems.\cite{Fukuda:2013sf}
148  
149 < \begin{figure}[h!]
149 > \begin{figure}
150    \centering
151 <  \includegraphics[width=0.50 \textwidth]{chargesystem.pdf}
152 <  \caption{Top: NaCl crystal showing how spherical truncation can
153 <    breaking effective charge ordering, and how complete \ce{(NaCl)4}
154 <    molecules interact with the central ion.  Bottom: A dipolar
155 <    crystal exhibiting similar behavior and illustrating how the
156 <    effective dipole-octupole interactions can be disrupted by
157 <    spherical truncation.}
158 <  \label{fig:NaCl}
151 >  \includegraphics[width=\linewidth]{schematic.pdf}
152 >  \caption{Top: Ionic systems exhibit local clustering of dissimilar
153 >    charges (in the smaller grey circle), so interactions are
154 >    effectively charge-multipole at longer distances.  With hard
155 >    cutoffs, motion of individual charges in and out of the cutoff
156 >    sphere can break the effective multipolar ordering.  Bottom:
157 >    dipolar crystals and fluids have a similar effective
158 >    \textit{quadrupolar} ordering (in the smaller grey circles), and
159 >    orientational averaging helps to reduce the effective range of the
160 >    interactions in the fluid.  Placement of reversed image multipoles
161 >    on the surface of the cutoff sphere recovers the effective
162 >    higher-order multipole behavior.}
163 >  \label{fig:schematic}
164   \end{figure}
165  
166   The direct truncation of interactions at a cutoff radius creates
167 < truncation defects. Wolf \textit{et al.} further argued that
167 > truncation defects. Wolf \textit{et al.}  argued that
168   truncation errors are due to net charge remaining inside the cutoff
169   sphere.\cite{Wolf:1999dn} To neutralize this charge they proposed
170   placing an image charge on the surface of the cutoff sphere for every
# Line 178 | Line 184 | potential is found to be decreasing as $r^{-5}$. If on
184  
185   Considering the interaction of one central ion in an ionic crystal
186   with a portion of the crystal at some distance, the effective Columbic
187 < potential is found to be decreasing as $r^{-5}$. If one views the
188 < \ce{NaCl} crystal as simple cubic (SC) structure with an octupolar
187 > potential is found to decrease as $r^{-5}$. If one views the \ce{NaCl}
188 > crystal as a simple cubic (SC) structure with an octupolar
189   \ce{(NaCl)4} basis, the electrostatic energy per ion converges more
190   rapidly to the Madelung energy than the dipolar
191   approximation.\cite{Wolf92} To find the correct Madelung constant,
192   Lacman suggested that the NaCl structure could be constructed in a way
193   that the finite crystal terminates with complete \ce{(NaCl)4}
194 < molecules.\cite{Lacman65} Any charge in a NaCl crystal is surrounded
195 < by opposite charges. Similarly for each pair of charges, there is an
196 < opposite pair of charge adjacent to it.  The central ion sees what is
197 < effectively a set of octupoles at large distances. These facts suggest
192 < that the Madelung constants are relatively short ranged for perfect
193 < ionic crystals.\cite{Wolf:1999dn}
194 > molecules.\cite{Lacman65} The central ion sees what is effectively a
195 > set of octupoles at large distances. These facts suggest that the
196 > Madelung constants are relatively short ranged for perfect ionic
197 > crystals.\cite{Wolf:1999dn}
198  
199   One can make a similar argument for crystals of point multipoles. The
200   Luttinger and Tisza treatment of energy constants for dipolar lattices
# Line 208 | Line 212 | multipolar arrangements (see Fig. \ref{fig:NaCl}), cau
212   unstable.
213  
214   In ionic crystals, real-space truncation can break the effective
215 < multipolar arrangements (see Fig. \ref{fig:NaCl}), causing significant
216 < swings in the electrostatic energy as the cutoff radius is increased
217 < (or as individual ions move back and forth across the boundary).  This
218 < is why the image charges were necessary for the Wolf sum to exhibit
219 < rapid convergence.  Similarly, the real-space truncation of point
220 < multipole interactions breaks higher order multipole arrangements, and
221 < image multipoles are required for real-space treatments of
218 < electrostatic energies.
215 > multipolar arrangements (see Fig. \ref{fig:schematic}), causing
216 > significant swings in the electrostatic energy as individual ions move
217 > back and forth across the boundary.  This is why the image charges are
218 > necessary for the Wolf sum to exhibit rapid convergence.  Similarly,
219 > the real-space truncation of point multipole interactions breaks
220 > higher order multipole arrangements, and image multipoles are required
221 > for real-space treatments of electrostatic energies.
222  
223 + The shorter effective range of electrostatic interactions is not
224 + limited to perfect crystals, but can also apply in disordered fluids.
225 + Even at elevated temperatures, there is, on average, local charge
226 + balance in an ionic liquid, where each positive ion has surroundings
227 + dominated by negaitve ions and vice versa.  The reversed-charge images
228 + on the cutoff sphere that are integral to the Wolf and DSF approaches
229 + retain the effective multipolar interactions as the charges traverse
230 + the cutoff boundary.
231 +
232 + In multipolar fluids (see Fig. \ref{fig:schematic}) there is
233 + significant orientational averaging that additionally reduces the
234 + effect of long-range multipolar interactions.  The image multipoles
235 + that are introduced in the TSF, GSF, and SP methods mimic this effect
236 + and reduce the effective range of the multipolar interactions as
237 + interacting molecules traverse each other's cutoff boundaries.
238 +
239   % Because of this reason, although the nature of electrostatic
240   % interaction short ranged, the hard cutoff sphere creates very large
241   % fluctuation in the electrostatic energy for the perfect crystal. In
# Line 273 | Line 292 | multipoles up to octupolar
292   rough approximation.  Atomic sites can also be assigned point
293   multipoles and polarizabilities to increase the accuracy of the
294   molecular model.  Recently, water has been modeled with point
295 < multipoles up to octupolar
296 < order.\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} Atom-centered point
295 > multipoles up to octupolar order using the soft sticky
296 > dipole-quadrupole-octupole (SSDQO)
297 > model.\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} Atom-centered point
298   multipoles up to quadrupolar order have also been coupled with point
299   polarizabilities in the high-quality AMOEBA and iAMOEBA water
300 < models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk}.  But
300 > models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk} But
301   using point multipole with the real space truncation without
302   accounting for multipolar neutrality will create energy conservation
303   issues in molecular dynamics (MD) simulations.
# Line 317 | Line 337 | where the multipole operator for site $\bf a$,
337   \begin{equation}
338   U_{\bf{ab}}(r)=\hat{M}_{\bf a} \hat{M}_{\bf b} \frac{1}{r}  \label{kernel}.
339   \end{equation}
340 < where the multipole operator for site $\bf a$,
341 < \begin{equation}
342 < \hat{M}_{\bf a} = C_{\bf a} - D_{{\bf a}\alpha} \frac{\partial}{\partial r_{\alpha}}
343 < +  Q_{{\bf a}\alpha\beta}
324 < \frac{\partial^2}{\partial r_{\alpha} \partial r_{\beta}} + \dots
325 < \end{equation}
326 < is expressed in terms of the point charge, $C_{\bf a}$, dipole,
327 < $D_{{\bf a}\alpha}$, and quadrupole, $Q_{{\bf a}\alpha\beta}$, for
328 < object $\bf a$.  Note that in this work, we use the primitive
329 < quadrupole tensor, $Q_{a\alpha,\beta}=\frac{1}{2}\sum_{k\;in\;a}q_k
330 < r_{k\alpha}r_{k\beta}$ to represent point quadrupoles on a site.
340 > where the multipole operator for site $\bf a$, $\hat{M}_{\bf a}$, is
341 > expressed in terms of the point charge, $C_{\bf a}$, dipole, ${\bf D}_{\bf
342 >    a}$, and quadrupole, $\mathbf{Q}_{\bf a}$, for object
343 > $\bf a$, etc.
344  
345 < Interactions between multipoles can be expressed as higher derivatives
346 < of the bare Coulomb potential, so one way of ensuring that the forces
347 < and torques vanish at the cutoff distance is to include a larger
348 < number of terms in the truncated Taylor expansion, e.g.,
349 < %
350 < \begin{equation}
351 < f_n^{\text{shift}}(r)=\sum_{m=0}^{n+1} \frac {(r-r_c)^m}{m!} f^{(m)} \Big \lvert  _{r_c}  .
352 < \end{equation}
353 < %
354 < The combination of $f(r)$ with the shifted function is denoted $f_n(r)=f(r)-f_n^{\text{shift}}(r)$.
355 < Thus, for $f(r)=1/r$, we find
356 < %
357 < \begin{equation}
358 < f_1(r)=\frac{1}{r}- \frac{1}{r_c} + (r - r_c) \frac{1}{r_c^2} - \frac{(r-r_c)^2}{r_c^3} .
359 < \end{equation}
360 < This function is an approximate electrostatic potential that has
361 < vanishing second derivatives at the cutoff radius, making it suitable
362 < for shifting the forces and torques of charge-dipole interactions.
345 > % Interactions between multipoles can be expressed as higher derivatives
346 > % of the bare Coulomb potential, so one way of ensuring that the forces
347 > % and torques vanish at the cutoff distance is to include a larger
348 > % number of terms in the truncated Taylor expansion, e.g.,
349 > % %
350 > % \begin{equation}
351 > % f_n^{\text{shift}}(r)=\sum_{m=0}^{n+1} \frac {(r-r_c)^m}{m!} f^{(m)} \Big \lvert  _{r_c}  .
352 > % \end{equation}
353 > % %
354 > % The combination of $f(r)$ with the shifted function is denoted $f_n(r)=f(r)-f_n^{\text{shift}}(r)$.
355 > % Thus, for $f(r)=1/r$, we find
356 > % %
357 > % \begin{equation}
358 > % f_1(r)=\frac{1}{r}- \frac{1}{r_c} + (r - r_c) \frac{1}{r_c^2} - \frac{(r-r_c)^2}{r_c^3} .
359 > % \end{equation}
360 > % This function is an approximate electrostatic potential that has
361 > % vanishing second derivatives at the cutoff radius, making it suitable
362 > % for shifting the forces and torques of charge-dipole interactions.
363  
364 < In general, the TSF potential for any multipole-multipole interaction
365 < can be written
364 > The TSF potential for any multipole-multipole interaction can be
365 > written
366   \begin{equation}
367   U^{\text{TSF}}= (\text{prefactor}) (\text{derivatives}) f_n(r)
368   \label{generic}
369   \end{equation}
370 < with $n=0$ for charge-charge, $n=1$ for charge-dipole, $n=2$ for
371 < charge-quadrupole and dipole-dipole, $n=3$ for dipole-quadrupole, and
372 < $n=4$ for quadrupole-quadrupole.  To ensure smooth convergence of the
373 < energy, force, and torques, the required number of terms from Taylor
374 < series expansion in $f_n(r)$ must be performed for different
375 < multipole-multipole interactions.
370 > where $f_n(r)$ is a shifted kernel that is appropriate for the order
371 > of the interaction (see Ref. \onlinecite{PaperI}), with $n=0$ for
372 > charge-charge, $n=1$ for charge-dipole, $n=2$ for charge-quadrupole
373 > and dipole-dipole, $n=3$ for dipole-quadrupole, and $n=4$ for
374 > quadrupole-quadrupole.  To ensure smooth convergence of the energy,
375 > force, and torques, a Taylor expansion with $n$ terms must be
376 > performed at cutoff radius ($r_c$) to obtain $f_n(r)$.
377  
378 < To carry out the same procedure for a damped electrostatic kernel, we
379 < replace $1/r$ in the Coulomb potential with $\text{erfc}(\alpha r)/r$.
380 < Many of the derivatives of the damped kernel are well known from
381 < Smith's early work on multipoles for the Ewald
382 < summation.\cite{Smith82,Smith98}
378 > % To carry out the same procedure for a damped electrostatic kernel, we
379 > % replace $1/r$ in the Coulomb potential with $\text{erfc}(\alpha r)/r$.
380 > % Many of the derivatives of the damped kernel are well known from
381 > % Smith's early work on multipoles for the Ewald
382 > % summation.\cite{Smith82,Smith98}
383  
384 < Note that increasing the value of $n$ will add additional terms to the
385 < electrostatic potential, e.g., $f_2(r)$ includes orders up to
386 < $(r-r_c)^3/r_c^4$, and so on.  Successive derivatives of the $f_n(r)$
387 < functions are denoted $g_2(r) = f^\prime_2(r)$, $h_2(r) =
388 < f^{\prime\prime}_2(r)$, etc.  These higher derivatives are required
389 < for computing multipole energies, forces, and torques, and smooth
390 < cutoffs of these quantities can be guaranteed as long as the number of
391 < terms in the Taylor series exceeds the derivative order required.
384 > % Note that increasing the value of $n$ will add additional terms to the
385 > % electrostatic potential, e.g., $f_2(r)$ includes orders up to
386 > % $(r-r_c)^3/r_c^4$, and so on.  Successive derivatives of the $f_n(r)$
387 > % functions are denoted $g_2(r) = f^\prime_2(r)$, $h_2(r) =
388 > % f^{\prime\prime}_2(r)$, etc.  These higher derivatives are required
389 > % for computing multipole energies, forces, and torques, and smooth
390 > % cutoffs of these quantities can be guaranteed as long as the number of
391 > % terms in the Taylor series exceeds the derivative order required.
392  
393   For multipole-multipole interactions, following this procedure results
394 < in separate radial functions for each distinct orientational
395 < contribution to the potential, and ensures that the forces and torques
396 < from {\it each} of these contributions will vanish at the cutoff
397 < radius.  For example, the direct dipole dot product ($\mathbf{D}_{i}
398 < \cdot \mathbf{D}_{j}$) is treated differently than the dipole-distance
394 > in separate radial functions for each of the distinct orientational
395 > contributions to the potential, and ensures that the forces and
396 > torques from each of these contributions will vanish at the cutoff
397 > radius.  For example, the direct dipole dot product
398 > ($\mathbf{D}_{\bf a}
399 > \cdot \mathbf{D}_{\bf b}$) is treated differently than the dipole-distance
400   dot products:
401   \begin{equation}
402 < U_{D_{i}D_{j}}(r)= -\frac{1}{4\pi \epsilon_0} \left( \mathbf{D}_{i} \cdot
403 < \mathbf{D}_{j} \right) \frac{g_2(r)}{r}
404 < -\frac{1}{4\pi \epsilon_0}
405 < \left( \mathbf{D}_{i} \cdot \hat{r} \right)
406 < \left( \mathbf{D}_{j} \cdot \hat{r} \right) \left(h_2(r) -
392 <  \frac{g_2(r)}{r} \right)
402 > U_{D_{\bf a}D_{\bf b}}(r)= -\frac{1}{4\pi \epsilon_0} \left[ \left(
403 >  \mathbf{D}_{\bf a} \cdot
404 > \mathbf{D}_{\bf b} \right) v_{21}(r) +
405 > \left( \mathbf{D}_{\bf a} \cdot \hat{r} \right)
406 > \left( \mathbf{D}_{\bf b} \cdot \hat{r} \right) v_{22}(r) \right]
407   \end{equation}
408  
409 < The electrostatic forces and torques acting on the central multipole
410 < site due to another site within cutoff sphere are derived from
409 > For the Taylor shifted (TSF) method with the undamped kernel,
410 > $v_{21}(r) = -\frac{1}{r^3} + \frac{3 r}{r_c^4} - \frac{8}{r_c^3} +
411 > \frac{6}{r r_c^2}$ and $v_{22}(r) = \frac{3}{r^3} + \frac{3 r}{r_c^4}
412 > - \frac{6}{r r_c^2}$.  In these functions, one can easily see the
413 > connection to unmodified electrostatics as well as the smooth
414 > transition to zero in both these functions as $r\rightarrow r_c$.  The
415 > electrostatic forces and torques acting on the central multipole due
416 > to another site within the cutoff sphere are derived from
417   Eq.~\ref{generic}, accounting for the appropriate number of
418   derivatives. Complete energy, force, and torque expressions are
419   presented in the first paper in this series (Reference
# Line 401 | Line 421 | A second (and significantly simpler) method involves s
421  
422   \subsection{Gradient-shifted force (GSF)}
423  
424 < A second (and significantly simpler) method involves shifting the
425 < gradient of the raw coulomb potential for each particular multipole
424 > A second (and conceptually simpler) method involves shifting the
425 > gradient of the raw Coulomb potential for each particular multipole
426   order.  For example, the raw dipole-dipole potential energy may be
427   shifted smoothly by finding the gradient for two interacting dipoles
428   which have been projected onto the surface of the cutoff sphere
429   without changing their relative orientation,
430 < \begin{displaymath}
431 < U_{D_{i}D_{j}}(r_{ij})  = U_{D_{i}D_{j}}(r_{ij}) - U_{D_{i}D_{j}}(r_c)
432 <   - (r_{ij}-r_c) \hat{r}_{ij} \cdot
433 <  \vec{\nabla} V_{D_{i}D_{j}}(r) \Big \lvert _{r_c}
434 < \end{displaymath}
435 < Here the lab-frame orientations of the two dipoles, $\mathbf{D}_{i}$
436 < and $\mathbf{D}_{j}$, are retained at the cutoff distance (although
437 < the signs are reversed for the dipole that has been projected onto the
438 < cutoff sphere).  In many ways, this simpler approach is closer in
439 < spirit to the original shifted force method, in that it projects a
440 < neutralizing multipole (and the resulting forces from this multipole)
441 < onto a cutoff sphere. The resulting functional forms for the
442 < potentials, forces, and torques turn out to be quite similar in form
443 < to the Taylor-shifted approach, although the radial contributions are
444 < significantly less perturbed by the Gradient-shifted approach than
445 < they are in the Taylor-shifted method.
430 > \begin{equation}
431 > U_{D_{\bf a}D_{\bf b}}(r)  = U_{D_{\bf a}D_{\bf b}}(r) -
432 > U_{D_{\bf a} D_{\bf b}}(r_c)
433 >   - (r_{ab}-r_c) ~~~\hat{r}_{ab} \cdot
434 >  \nabla U_{D_{\bf a}D_{\bf b}}(r_c).
435 > \end{equation}
436 > Here the lab-frame orientations of the two dipoles, $\mathbf{D}_{\bf
437 >  a}$ and $\mathbf{D}_{\bf b}$, are retained at the cutoff distance
438 > (although the signs are reversed for the dipole that has been
439 > projected onto the cutoff sphere).  In many ways, this simpler
440 > approach is closer in spirit to the original shifted force method, in
441 > that it projects a neutralizing multipole (and the resulting forces
442 > from this multipole) onto a cutoff sphere. The resulting functional
443 > forms for the potentials, forces, and torques turn out to be quite
444 > similar in form to the Taylor-shifted approach, although the radial
445 > contributions are significantly less perturbed by the gradient-shifted
446 > approach than they are in the Taylor-shifted method.
447  
448 + For the gradient shifted (GSF) method with the undamped kernel,
449 + $v_{21}(r) = -\frac{1}{r^3} + \frac{3 r}{r_c^4} + \frac{4}{r_c^3}$ and
450 + $v_{22}(r) = \frac{3}{r^3} + \frac{9 r}{r_c^4} - \frac{12}{r_c^3}$.
451 + Again, these functions go smoothly to zero as $r\rightarrow r_c$, and
452 + because the Taylor expansion retains only one term, they are
453 + significantly less perturbed than the TSF functions.
454 +
455   In general, the gradient shifted potential between a central multipole
456   and any multipolar site inside the cutoff radius is given by,
457   \begin{equation}
458 < U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) -
459 < U(\mathbf{r}_c,\hat{\mathbf{a}}, \hat{\mathbf{b}}) - (r-r_c) \hat{r}
460 < \cdot \nabla U(\mathbf{r},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \Big \lvert  _{r_c} \right]
458 >  U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) -
459 >    U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) - (r-r_c) \hat{\mathbf{r}}
460 >    \cdot \nabla U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \right]
461   \label{generic2}
462   \end{equation}
463   where the sum describes a separate force-shifting that is applied to
464 < each orientational contribution to the energy.
464 > each orientational contribution to the energy.  In this expression,
465 > $\hat{\mathbf{r}}$ is the unit vector connecting the two multipoles
466 > ($a$ and $b$) in space, and $\hat{\mathbf{a}}$ and $\hat{\mathbf{b}}$
467 > represent the orientations the multipoles.
468  
469   The third term converges more rapidly than the first two terms as a
470   function of radius, hence the contribution of the third term is very
471   small for large cutoff radii.  The force and torque derived from
472 < equation \ref{generic2} are consistent with the energy expression and
472 > Eq. \ref{generic2} are consistent with the energy expression and
473   approach zero as $r \rightarrow r_c$.  Both the GSF and TSF methods
474   can be considered generalizations of the original DSF method for
475   higher order multipole interactions. GSF and TSF are also identical up
# Line 446 | Line 477 | GSF potential are presented in the first paper in this
477   the energy, force and torque for higher order multipole-multipole
478   interactions. Complete energy, force, and torque expressions for the
479   GSF potential are presented in the first paper in this series
480 < (Reference~\onlinecite{PaperI})
480 > (Reference~\onlinecite{PaperI}).
481  
482  
483   \subsection{Shifted potential (SP) }
# Line 459 | Line 490 | U_{SP}(\vec r)=\sum U(\vec r) - U(\vec r_c)
490   interactions with the central multipole and the image. This
491   effectively shifts the total potential to zero at the cutoff radius,
492   \begin{equation}
493 < U_{SP}(\vec r)=\sum U(\vec r) - U(\vec r_c)
493 > U^{\text{SP}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) -
494 > U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \right]
495   \label{eq:SP}
496   \end{equation}          
497   where the sum describes separate potential shifting that is done for
# Line 471 | Line 503 | The potential energy between a central multipole and o
503   multipoles that reorient after leaving the cutoff sphere can re-enter
504   the cutoff sphere without perturbing the total energy.
505  
506 < The potential energy between a central multipole and other multipolar
507 < sites then goes smoothly to zero as $r \rightarrow r_c$. However, the
508 < force and torque obtained from the shifted potential (SP) are
509 < discontinuous at $r_c$. Therefore, MD simulations will still
510 < experience energy drift while operating under the SP potential, but it
511 < may be suitable for Monte Carlo approaches where the configurational
512 < energy differences are the primary quantity of interest.
506 > For the shifted potential (SP) method with the undamped kernel,
507 > $v_{21}(r) = -\frac{1}{r^3} + \frac{1}{r_c^3}$ and $v_{22}(r) =
508 > \frac{3}{r^3} - \frac{3}{r_c^3}$.  The potential energy between a
509 > central multipole and other multipolar sites goes smoothly to zero as
510 > $r \rightarrow r_c$.  However, the force and torque obtained from the
511 > shifted potential (SP) are discontinuous at $r_c$.  MD simulations
512 > will still experience energy drift while operating under the SP
513 > potential, but it may be suitable for Monte Carlo approaches where the
514 > configurational energy differences are the primary quantity of
515 > interest.
516  
517 < \subsection{The Self term}
517 > \subsection{The Self Term}
518   In the TSF, GSF, and SP methods, a self-interaction is retained for
519   the central multipole interacting with its own image on the surface of
520   the cutoff sphere.  This self interaction is nearly identical with the
# Line 501 | Line 536 | in the test-cases are given in table~\ref{tab:pars}.
536   used the multipolar Ewald sum as a reference method for comparing
537   energies, forces, and torques for molecular models that mimic
538   disordered and ordered condensed-phase systems.  The parameters used
539 < in the test-cases are given in table~\ref{tab:pars}.
539 > in the test cases are given in table~\ref{tab:pars}.
540  
541   \begin{table}
542   \label{tab:pars}
# Line 519 | Line 554 | in the test-cases are given in table~\ref{tab:pars}.
554   & (\AA) & (kcal/mol) & (e) & (debye) & \multicolumn{3}{c|}{(debye \AA)} & (amu) & \multicolumn{3}{c}{(amu
555   \AA\textsuperscript{2})} \\ \hline
556      Soft Dipolar fluid & 3.051 & 0.152 &  & 2.35 & & & & 18.0153 & 1.77&0.6145& 1.155 \\
557 <    Soft Dipolar solid & 2.837 & 1.0   &  & 2.35 & & & & 10,000  & 17.6 &17.6 & 0 \\
557 >    Soft Dipolar solid & 2.837 & 1.0   &  & 2.35 & & & & $10^4$  & 17.6 &17.6 & 0 \\
558   Soft Quadrupolar fluid & 3.051 & 0.152 &  &  & -1&-1&-2.5 & 18.0153 & 1.77&0.6145&1.155  \\
559 < Soft Quadrupolar solid & 2.837 & 1.0   &  &  & -1&-1&-2.5 & 10,000  & 17.6&17.6&0 \\
559 > Soft Quadrupolar solid & 2.837 & 1.0   &  &  & -1&-1&-2.5 & $10^4$  & 17.6&17.6&0 \\
560        SSDQ water  & 3.051 & 0.152 &  & 2.35 & -1.35&0&-0.68 & 18.0153 & 1.77&0.6145&1.155 \\
561                \ce{Na+} & 2.579 & 0.118 & +1& & & & & 22.99 & & &\\
562                \ce{Cl-} & 4.445 & 0.1   & -1& & & & & 35.4527& & & \\ \hline
# Line 546 | Line 581 | and have been compared with the values obtaine from th
581   electrostatic energy, as well as the electrostatic contributions to
582   the force and torque on each molecule.  These quantities have been
583   computed using the SP, TSF, and GSF methods, as well as a hard cutoff,
584 < and have been compared with the values obtaine from the multipolar
585 < Ewald sum.  In Mote Carlo (MC) simulations, the energy differences
584 > and have been compared with the values obtained from the multipolar
585 > Ewald sum.  In Monte Carlo (MC) simulations, the energy differences
586   between two configurations is the primary quantity that governs how
587   the simulation proceeds. These differences are the most imporant
588   indicators of the reliability of a method even if the absolute
# Line 594 | Line 629 | To sample independent configurations of multipolar cry
629   recomputed at each time step.
630  
631   \subsection{Model systems}
632 < To sample independent configurations of multipolar crystals, a body
633 < centered cubic (bcc) crystal which is a minimum energy structure for
634 < point dipoles was generated using 3,456 molecules.  The multipoles
635 < were translationally locked in their respective crystal sites for
636 < equilibration at a relatively low temperature (50K), so that dipoles
637 < or quadrupoles could freely explore all accessible orientations.  The
638 < translational constraints were removed, and the crystals were
639 < simulated for 10 ps in the microcanonical (NVE) ensemble with an
640 < average temperature of 50 K.  Configurations were sampled at equal
641 < time intervals for the comparison of the configurational energy
642 < differences.  The crystals were not simulated close to the melting
643 < points in order to avoid translational deformation away of the ideal
644 < lattice geometry.
645 <
646 < For dipolar, quadrupolar, and mixed-multipole liquid simulations, each
647 < system was created with 2048 molecules oriented randomly.  These were
632 > To sample independent configurations of the multipolar crystals, body
633 > centered cubic (bcc) crystals, which exhibit the minimum energy
634 > structures for point dipoles, were generated using 3,456 molecules.
635 > The multipoles were translationally locked in their respective crystal
636 > sites for equilibration at a relatively low temperature (50K) so that
637 > dipoles or quadrupoles could freely explore all accessible
638 > orientations.  The translational constraints were then removed, the
639 > systems were re-equilibrated, and the crystals were simulated for an
640 > additional 10 ps in the microcanonical (NVE) ensemble with an average
641 > temperature of 50 K.  The balance between moments of inertia and
642 > particle mass were chosen to allow orientational sampling without
643 > significant translational motion.  Configurations were sampled at
644 > equal time intervals in order to compare configurational energy
645 > differences.  The crystals were simulated far from the melting point
646 > in order to avoid translational deformation away of the ideal lattice
647 > geometry.
648  
649 < system with 2,048 molecules simulated for 1ns in NVE ensemble at 300 K
650 < temperature after equilibration.  We collected 250 different
651 < configurations in equal interval of time. For the ions mixed liquid
652 < system, we converted 48 different molecules into 24 \ce{Na+} and 24
653 < \ce{Cl-} ions and equilibrated. After equilibration, the system was run
654 < at the same environment for 1ns and 250 configurations were
655 < collected. While comparing energies, forces, and torques with Ewald
656 < method, Lennard-Jones potentials were turned off and purely
657 < electrostatic interaction had been compared.
649 > For dipolar, quadrupolar, and mixed-multipole \textit{liquid}
650 > simulations, each system was created with 2,048 randomly-oriented
651 > molecules.  These were equilibrated at a temperature of 300K for 1 ns.
652 > Each system was then simulated for 1 ns in the microcanonical (NVE)
653 > ensemble.  We collected 250 different configurations at equal time
654 > intervals. For the liquid system that included ionic species, we
655 > converted 48 randomly-distributed molecules into 24 \ce{Na+} and 24
656 > \ce{Cl-} ions and re-equilibrated. After equilibration, the system was
657 > run under the same conditions for 1 ns. A total of 250 configurations
658 > were collected. In the following comparisons of energies, forces, and
659 > torques, the Lennard-Jones potentials were turned off and only the
660 > purely electrostatic quantities were compared with the same values
661 > obtained via the Ewald sum.
662  
663   \subsection{Accuracy of Energy Differences, Forces and Torques}
664   The pairwise summation techniques (outlined above) were evaluated for
# Line 633 | Line 672 | we used least square regressions analysiss for the six
672   should be identical for all methods.
673  
674   Since none of the real-space methods provide exact energy differences,
675 < we used least square regressions analysiss for the six different
675 > we used least square regressions analysis for the six different
676   molecular systems to compare $\Delta E$ from Hard, SP, GSF, and TSF
677   with the multipolar Ewald reference method.  Unitary results for both
678   the correlation (slope) and correlation coefficient for these
# Line 644 | Line 683 | also been compared by using least squares regression a
683   configurations and 250 configurations were recorded for comparison.
684   Each system provided 31,125 energy differences for a total of 186,750
685   data points.  Similarly, the magnitudes of the forces and torques have
686 < also been compared by using least squares regression analyses. In the
686 > also been compared using least squares regression analysis. In the
687   forces and torques comparison, the magnitudes of the forces acting in
688   each molecule for each configuration were evaluated. For example, our
689   dipolar liquid simulation contains 2048 molecules and there are 250
# Line 829 | Line 868 | perturbations are minimal, particularly for moderate d
868   molecules inside each other's cutoff spheres in order to correct the
869   energy conservation issues, and this perturbation is evident in the
870   statistics accumulated for the molecular forces.  The GSF
871 < perturbations are minimal, particularly for moderate damping and and
871 > perturbations are minimal, particularly for moderate damping and
872   commonly-used cutoff values ($r_c = 12$\AA).  The TSF method shows
873   reasonable agreement in the correlation coefficient but again the
874   systematic error in the forces is concerning if replication of Ewald
# Line 886 | Line 925 | directionality is shown in terms of circular variance
925   these quantities. Force and torque vectors for all six systems were
926   analyzed using Fisher statistics, and the quality of the vector
927   directionality is shown in terms of circular variance
928 < ($\mathrm{Var}(\theta$) in figure
928 > ($\mathrm{Var}(\theta)$) in figure
929   \ref{fig:slopeCorr_circularVariance}. The force and torque vectors
930   from the new real-space methods exhibit nearly-ideal Fisher probability
931   distributions (Eq.~\ref{eq:pdf}). Both the hard and SP cutoff methods
# Line 941 | Line 980 | conservation (drift less than $10^{-6}$ kcal / mol / n
980   energy over time, $\delta E_1$, and the standard deviation of energy
981   fluctuations around this drift $\delta E_0$.  Both of the
982   shifted-force methods (GSF and TSF) provide excellent energy
983 < conservation (drift less than $10^{-6}$ kcal / mol / ns / particle),
983 > conservation (drift less than $10^{-5}$ kcal / mol / ns / particle),
984   while the hard cutoff is essentially unusable for molecular dynamics.
985   SP provides some benefit over the hard cutoff because the energetic
986   jumps that happen as particles leave and enter the cutoff sphere are
# Line 956 | Line 995 | $k$-space cutoff values.
995  
996   \begin{figure}
997    \centering
998 <  \includegraphics[width=\textwidth]{newDrift.pdf}
998 >  \includegraphics[width=\textwidth]{newDrift_12.pdf}
999   \label{fig:energyDrift}        
1000   \caption{Analysis of the energy conservation of the real-space
1001    electrostatic methods. $\delta \mathrm{E}_1$ is the linear drift in
1002 <  energy over time and $\delta \mathrm{E}_0$ is the standard deviation
1003 <  of energy fluctuations around this drift.  All simulations were of a
1004 <  2000-molecule simulation of SSDQ water with 48 ionic charges at 300
1005 <  K starting from the same initial configuration. All runs utilized
1006 <  the same real-space cutoff, $r_c = 12$\AA.}
1002 >  energy over time (in kcal / mol / particle / ns) and $\delta
1003 >  \mathrm{E}_0$ is the standard deviation of energy fluctuations
1004 >  around this drift (in kcal / mol / particle).  All simulations were
1005 >  of a 2000-molecule simulation of SSDQ water with 48 ionic charges at
1006 >  300 K starting from the same initial configuration. All runs
1007 >  utilized the same real-space cutoff, $r_c = 12$\AA.}
1008   \end{figure}
1009  
1010  
# Line 1044 | Line 1084 | real-space cutoff boundary.
1084   handling of energies, forces, and torques as multipoles cross the
1085   real-space cutoff boundary.
1086  
1087 + \begin{acknowledgments}
1088 +  JDG acknowledges helpful discussions with Christopher
1089 +  Fennell. Support for this project was provided by the National
1090 +  Science Foundation under grant CHE-1362211. Computational time was
1091 +  provided by the Center for Research Computing (CRC) at the
1092 +  University of Notre Dame.
1093 + \end{acknowledgments}
1094 +
1095   %\bibliographystyle{aip}
1096   \newpage
1097   \bibliography{references}

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