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22 \begin{document}
23
24 \title{On the structural and transport properties of the soft sticky
25 dipole (SSD) and related single point water models}
26
27 \author{Christopher J. Fennell and J. Daniel Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
28 Department of Chemistry and Biochemistry\\ University of Notre Dame\\
29 Notre Dame, Indiana 46556}
30
31 \date{\today}
32
33 \maketitle
34
35 \begin{abstract}
36 The density maximum and temperature dependence of the self-diffusion
37 constant were investigated for the soft sticky dipole (SSD) water
38 model and two related re-parameterizations of this single-point model.
39 A combination of microcanonical and isobaric-isothermal molecular
40 dynamics simulations were used to calculate these properties, both
41 with and without the use of reaction field to handle long-range
42 electrostatics. The isobaric-isothermal (NPT) simulations of the
43 melting of both ice-$I_h$ and ice-$I_c$ showed a density maximum near
44 260 K. In most cases, the use of the reaction field resulted in
45 calculated densities which were were significantly lower than
46 experimental densities. Analysis of self-diffusion constants shows
47 that the original SSD model captures the transport properties of
48 experimental water very well in both the normal and super-cooled
49 liquid regimes. We also present our re-parameterized versions of SSD
50 for use both with the reaction field or without any long-range
51 electrostatic corrections. These are called the SSD/RF and SSD/E
52 models respectively. These modified models were shown to maintain or
53 improve upon the experimental agreement with the structural and
54 transport properties that can be obtained with either the original SSD
55 or the density corrected version of the original model (SSD1).
56 Additionally, a novel low-density ice structure is presented
57 which appears to be the most stable ice structure for the entire SSD
58 family.
59 \end{abstract}
60
61 \newpage
62
63 %\narrowtext
64
65
66 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
67 % BODY OF TEXT
68 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
69
70 \section{Introduction}
71
72 One of the most important tasks in the simulation of biochemical
73 systems is the proper depiction of the aqueous environment of the
74 molecules of interest. In some cases (such as in the simulation of
75 phospholipid bilayers), the majority of the calculations that are
76 performed involve interactions with or between solvent molecules.
77 Thus, the properties one may observe in biochemical simulations are
78 going to be highly dependent on the physical properties of the water
79 model that is chosen.
80
81 There is an especially delicate balance between computational
82 efficiency and the ability of the water model to accurately predict
83 the properties of bulk
84 water.\cite{Jorgensen83,Berendsen87,Jorgensen00} For example, the
85 TIP5P model improves on the structural and transport properties of
86 water relative to the previous TIP models, yet this comes at a greater
87 than 50\% increase in computational
88 cost.\cite{Jorgensen01,Jorgensen00}
89
90 One recently developed model that largely succeeds in retaining the
91 accuracy of bulk properties while greatly reducing the computational
92 cost is the Soft Sticky Dipole (SSD) water
93 model.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03} The SSD model was
94 developed by Ichiye \emph{et al.} as a modified form of the
95 hard-sphere water model proposed by Bratko, Blum, and
96 Luzar.\cite{Bratko85,Bratko95} SSD is a {\it single point} model which
97 has an interaction site that is both a point dipole along with a
98 Lennard-Jones core. However, since the normal aligned and
99 anti-aligned geometries favored by point dipoles are poor mimics of
100 local structure in liquid water, a short ranged ``sticky'' potential
101 is also added. The sticky potential directs the molecules to assume
102 the proper hydrogen bond orientation in the first solvation
103 shell.
104
105 The interaction between two SSD water molecules \emph{i} and \emph{j}
106 is given by the potential
107 \begin{equation}
108 u_{ij} = u_{ij}^{LJ} (r_{ij})\ + u_{ij}^{dp}
109 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)\ +
110 u_{ij}^{sp}
111 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j),
112 \end{equation}
113 where the ${\bf r}_{ij}$ is the position vector between molecules
114 \emph{i} and \emph{j} with magnitude $r_{ij}$, and
115 ${\bf \Omega}_i$ and ${\bf \Omega}_j$ represent the orientations of
116 the two molecules. The Lennard-Jones and dipole interactions are given
117 by the following familiar forms:
118 \begin{equation}
119 u_{ij}^{LJ}(r_{ij}) = 4\epsilon
120 \left[\left(\frac{\sigma}{r_{ij}}\right)^{12}-\left(\frac{\sigma}{r_{ij}}\right)^{6}\right]
121 \ ,
122 \end{equation}
123 and
124 \begin{equation}
125 u_{ij}^{dp} = \frac{|\mu_i||\mu_j|}{4 \pi \epsilon_0 r_{ij}^3} \left(
126 \hat{\bf u}_i \cdot \hat{\bf u}_j - 3(\hat{\bf u}_i\cdot\hat{\bf
127 r}_{ij})(\hat{\bf u}_j\cdot\hat{\bf r}_{ij}) \right)\ ,
128 \end{equation}
129 where $\hat{\bf u}_i$ and $\hat{\bf u}_j$ are the unit vectors along
130 the dipoles of molecules $i$ and $j$ respectively. $|\mu_i|$ and
131 $|\mu_j|$ are the strengths of the dipole moments, and $\hat{\bf
132 r}_{ij}$ is the unit vector pointing from molecule $j$ to molecule
133 $i$.
134
135 The sticky potential is somewhat less familiar:
136 \begin{equation}
137 u_{ij}^{sp}
138 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j) =
139 \frac{\nu_0}{2}[s(r_{ij})w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)
140 + s^\prime(r_{ij})w^\prime({\bf r}_{ij},{\bf \Omega}_i,{\bf
141 \Omega}_j)]\ .
142 \label{stickyfunction}
143 \end{equation}
144 Here, $\nu_0$ is a strength parameter for the sticky potential, and
145 $s$ and $s^\prime$ are cubic switching functions which turn off the
146 sticky interaction beyond the first solvation shell. The $w$ function
147 can be thought of as an attractive potential with tetrahedral
148 geometry:
149 \begin{equation}
150 w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)=\sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij},
151 \end{equation}
152 while the $w^\prime$ function counters the normal aligned and
153 anti-aligned structures favored by point dipoles:
154 \begin{equation}
155 w^\prime({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j) = (\cos\theta_{ij}-0.6)^2(\cos\theta_{ij}+0.8)^2-w^\circ,
156 \end{equation}
157 It should be noted that $w$ is proportional to the sum of the $Y_3^2$
158 and $Y_3^{-2}$ spherical harmonics (a linear combination which
159 enhances the tetrahedral geometry for hydrogen bonded structures),
160 while $w^\prime$ is a purely empirical function. A more detailed
161 description of the functional parts and variables in this potential
162 can be found in the original SSD
163 articles.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03}
164
165 Since SSD is a single-point {\it dipolar} model, the force
166 calculations are simplified significantly relative to the standard
167 {\it charged} multi-point models. In the original Monte Carlo
168 simulations using this model, Ichiye {\it et al.} reported that using
169 SSD decreased computer time by a factor of 6-7 compared to other
170 models.\cite{Ichiye96} What is most impressive is that this savings
171 did not come at the expense of accurate depiction of the liquid state
172 properties. Indeed, SSD maintains reasonable agreement with the Soper
173 data for the structural features of liquid
174 water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties
175 exhibited by SSD agree with experiment better than those of more
176 computationally expensive models (like TIP3P and
177 SPC/E).\cite{Ichiye99} The combination of speed and accurate depiction
178 of solvent properties makes SSD a very attractive model for the
179 simulation of large scale biochemical simulations.
180
181 One feature of the SSD model is that it was parameterized for use with
182 the Ewald sum to handle long-range interactions. This would normally
183 be the best way of handling long-range interactions in systems that
184 contain other point charges. However, our group has recently become
185 interested in systems with point dipoles as mimics for neutral, but
186 polarized regions on molecules (e.g. the zwitterionic head group
187 regions of phospholipids). If the system of interest does not contain
188 point charges, the Ewald sum and even particle-mesh Ewald become
189 computational bottlenecks. Their respective ideal $N^\frac{3}{2}$ and
190 $N\log N$ calculation scaling orders for $N$ particles can become
191 prohibitive when $N$ becomes large.\cite{Darden99} In applying this
192 water model in these types of systems, it would be useful to know its
193 properties and behavior under the more computationally efficient
194 reaction field (RF) technique, or even with a simple cutoff. This
195 study addresses these issues by looking at the structural and
196 transport behavior of SSD over a variety of temperatures with the
197 purpose of utilizing the RF correction technique. We then suggest
198 modifications to the parameters that result in more realistic bulk
199 phase behavior. It should be noted that in a recent publication, some
200 of the original investigators of the SSD water model have suggested
201 adjustments to the SSD water model to address abnormal density
202 behavior (also observed here), calling the corrected model
203 SSD1.\cite{Ichiye03} In what follows, we compare our
204 reparamaterization of SSD with both the original SSD and SSD1 models
205 with the goal of improving the bulk phase behavior of an SSD-derived
206 model in simulations utilizing the Reaction Field.
207
208 \section{Methods}
209
210 Long-range dipole-dipole interactions were accounted for in this study
211 by using either the reaction field method or by resorting to a simple
212 cubic switching function at a cutoff radius. The reaction field
213 method was actually first used in Monte Carlo simulations of liquid
214 water.\cite{Barker73} Under this method, the magnitude of the reaction
215 field acting on dipole $i$ is
216 \begin{equation}
217 \mathcal{E}_{i} = \frac{2(\varepsilon_{s} - 1)}{2\varepsilon_{s} + 1}
218 \frac{1}{r_{c}^{3}} \sum_{j\in{\mathcal{R}}} {\bf \mu}_{j} f(r_{ij})\ ,
219 \label{rfequation}
220 \end{equation}
221 where $\mathcal{R}$ is the cavity defined by the cutoff radius
222 ($r_{c}$), $\varepsilon_{s}$ is the dielectric constant imposed on the
223 system (80 in the case of liquid water), ${\bf \mu}_{j}$ is the dipole
224 moment vector of particle $j$ and $f(r_{ij})$ is a cubic switching
225 function.\cite{AllenTildesley} The reaction field contribution to the
226 total energy by particle $i$ is given by $-\frac{1}{2}{\bf
227 \mu}_{i}\cdot\mathcal{E}_{i}$ and the torque on dipole $i$ by ${\bf
228 \mu}_{i}\times\mathcal{E}_{i}$.\cite{AllenTildesley} Use of the reaction
229 field is known to alter the bulk orientational properties, such as the
230 dielectric relaxation time. There is particular sensitivity of this
231 property on changes in the length of the cutoff
232 radius.\cite{Berendsen98} This variable behavior makes reaction field
233 a less attractive method than the Ewald sum. However, for very large
234 systems, the computational benefit of reaction field is dramatic.
235
236 We have also performed a companion set of simulations {\it without} a
237 surrounding dielectric (i.e. using a simple cubic switching function
238 at the cutoff radius) and as a result we have two reparamaterizations
239 of SSD which could be used either with or without the Reaction Field
240 turned on.
241
242 Simulations to obtain the preferred density were performed in the
243 isobaric-isothermal (NPT) ensemble, while all dynamical properties
244 were obtained from microcanonical (NVE) simulations done at densities
245 matching the NPT density for a particular target temperature. The
246 constant pressure simulations were implemented using an integral
247 thermostat and barostat as outlined by Hoover.\cite{Hoover85,Hoover86}
248 All molecules were treated as non-linear rigid bodies. Vibrational
249 constraints are not necessary in simulations of SSD, because there are
250 no explicit hydrogen atoms, and thus no molecular vibrational modes
251 need to be considered.
252
253 Integration of the equations of motion was carried out using the
254 symplectic splitting method proposed by Dullweber {\it et
255 al.}\cite{Dullweber1997} Our reason for selecting this integrator
256 centers on poor energy conservation of rigid body dynamics using
257 traditional quaternion integration.\cite{Evans77,Evans77b} While quaternions
258 may work well for orientational motion under NVT or NPT integrators,
259 our limits on energy drift in the microcanonical ensemble were quite
260 strict, and the drift under quaternions was substantially greater than
261 in the symplectic splitting method. This steady drift in the total
262 energy has also been observed by Kol {\it et al.}\cite{Laird97}
263
264 The key difference in the integration method proposed by Dullweber
265 \emph{et al.} is that the entire rotation matrix is propagated from
266 one time step to the next. The additional memory required by the
267 algorithm is inconsequential on modern computers, and translating the
268 rotation matrix into quaternions for storage purposes makes trajectory
269 data quite compact.
270
271 The symplectic splitting method allows for Verlet style integration of
272 both translational and orientational motion of rigid bodies. In this
273 integration method, the orientational propagation involves a sequence
274 of matrix evaluations to update the rotation
275 matrix.\cite{Dullweber1997} These matrix rotations are more costly
276 than the simpler arithmetic quaternion propagation. With the same time
277 step, a 1000 SSD particle simulation shows an average 7\% increase in
278 computation time using the symplectic step method in place of
279 quaternions. The additional expense per step is justified when one
280 considers the ability to use time steps that are nearly twice as large
281 under symplectic splitting than would be usable under quaternion
282 dynamics. The energy conservation of the two methods using a number
283 of different time steps is illustrated in figure
284 \ref{timestep}.
285
286 \begin{figure}
287 \begin{center}
288 \epsfxsize=6in
289 \epsfbox{timeStep.epsi}
290 \caption{Energy conservation using both quaternion based integration and
291 the symplectic step method proposed by Dullweber \emph{et al.} with
292 increasing time step. The larger time step plots are shifted from the
293 true energy baseline (that of $\Delta t$ = 0.1 fs) for clarity.}
294 \label{timestep}
295 \end{center}
296 \end{figure}
297
298 In figure \ref{timestep}, the resulting energy drift at various time
299 steps for both the symplectic step and quaternion integration schemes
300 is compared. All of the 1000 SSD particle simulations started with
301 the same configuration, and the only difference was the method used to
302 handle orientational motion. At time steps of 0.1 and 0.5 fs, both
303 methods for propagating the orientational degrees of freedom conserve
304 energy fairly well, with the quaternion method showing a slight energy
305 drift over time in the 0.5 fs time step simulation. At time steps of 1
306 and 2 fs, the energy conservation benefits of the symplectic step
307 method are clearly demonstrated. Thus, while maintaining the same
308 degree of energy conservation, one can take considerably longer time
309 steps, leading to an overall reduction in computation time.
310
311 Energy drift in the symplectic step simulations was unnoticeable for
312 time steps up to 3 fs. A slight energy drift on the
313 order of 0.012 kcal/mol per nanosecond was observed at a time step of
314 4 fs, and as expected, this drift increases dramatically
315 with increasing time step. To insure accuracy in our microcanonical
316 simulations, time steps were set at 2 fs and kept at this value for
317 constant pressure simulations as well.
318
319 Proton-disordered ice crystals in both the $I_h$ and $I_c$ lattices
320 were generated as starting points for all simulations. The $I_h$
321 crystals were formed by first arranging the centers of mass of the SSD
322 particles into a ``hexagonal'' ice lattice of 1024 particles. Because
323 of the crystal structure of $I_h$ ice, the simulation box assumed an
324 orthorhombic shape with an edge length ratio of approximately
325 1.00$\times$1.06$\times$1.23. The particles were then allowed to
326 orient freely about fixed positions with angular momenta randomized at
327 400 K for varying times. The rotational temperature was then scaled
328 down in stages to slowly cool the crystals to 25 K. The particles were
329 then allowed to translate with fixed orientations at a constant
330 pressure of 1 atm for 50 ps at 25 K. Finally, all constraints were
331 removed and the ice crystals were allowed to equilibrate for 50 ps at
332 25 K and a constant pressure of 1 atm. This procedure resulted in
333 structurally stable $I_h$ ice crystals that obey the Bernal-Fowler
334 rules.\cite{Bernal33,Rahman72} This method was also utilized in the
335 making of diamond lattice $I_c$ ice crystals, with each cubic
336 simulation box consisting of either 512 or 1000 particles. Only
337 isotropic volume fluctuations were performed under constant pressure,
338 so the ratio of edge lengths remained constant throughout the
339 simulations.
340
341 \section{Results and discussion}
342
343 Melting studies were performed on the randomized ice crystals using
344 isobaric-isothermal (NPT) dynamics. During melting simulations, the
345 melting transition and the density maximum can both be observed,
346 provided that the density maximum occurs in the liquid and not the
347 supercooled regime. An ensemble average from five separate melting
348 simulations was acquired, each starting from different ice crystals
349 generated as described previously. All simulations were equilibrated
350 for 100 ps prior to a 200 ps data collection run at each temperature
351 setting. The temperature range of study spanned from 25 to 400 K, with
352 a maximum degree increment of 25 K. For regions of interest along this
353 stepwise progression, the temperature increment was decreased from 25
354 K to 10 and 5 K. The above equilibration and production times were
355 sufficient in that fluctuations in the volume autocorrelation function
356 were damped out in all simulations in under 20 ps.
357
358 \subsection{Density Behavior}
359
360 Our initial simulations focused on the original SSD water model, and
361 an average density versus temperature plot is shown in figure
362 \ref{dense1}. Note that the density maximum when using a reaction
363 field appears between 255 and 265 K. There were smaller fluctuations
364 in the density at 260 K than at either 255 or 265, so we report this
365 value as the location of the density maximum. Figure \ref{dense1} was
366 constructed using ice $I_h$ crystals for the initial configuration;
367 though not pictured, the simulations starting from ice $I_c$ crystal
368 configurations showed similar results, with a liquid-phase density
369 maximum in this same region (between 255 and 260 K).
370
371 \begin{figure}
372 \begin{center}
373 \epsfxsize=6in
374 \epsfbox{denseSSD.eps}
375 \caption{Density versus temperature for TIP4P [Ref. \citen{Jorgensen98b}],
376 TIP3P [Ref. \citen{Jorgensen98b}], SPC/E [Ref. \citen{Clancy94}], SSD
377 without Reaction Field, SSD, and experiment [Ref. \citen{CRC80}]. The
378 arrows indicate the change in densities observed when turning off the
379 reaction field. The the lower than expected densities for the SSD
380 model were what prompted the original reparameterization of SSD1
381 [Ref. \citen{Ichiye03}].}
382 \label{dense1}
383 \end{center}
384 \end{figure}
385
386 The density maximum for SSD compares quite favorably to other simple
387 water models. Figure \ref{dense1} also shows calculated densities of
388 several other models and experiment obtained from other
389 sources.\cite{Jorgensen98b,Clancy94,CRC80} Of the listed simple water
390 models, SSD has a temperature closest to the experimentally observed
391 density maximum. Of the {\it charge-based} models in
392 Fig. \ref{dense1}, TIP4P has a density maximum behavior most like that
393 seen in SSD. Though not included in this plot, it is useful
394 to note that TIP5P has a density maximum nearly identical to the
395 experimentally measured temperature.
396
397 It has been observed that liquid state densities in water are
398 dependent on the cutoff radius used both with and without the use of
399 reaction field.\cite{Berendsen98} In order to address the possible
400 effect of cutoff radius, simulations were performed with a dipolar
401 cutoff radius of 12.0 \AA\ to complement the previous SSD simulations,
402 all performed with a cutoff of 9.0 \AA. All of the resulting densities
403 overlapped within error and showed no significant trend toward lower
404 or higher densities as a function of cutoff radius, for simulations
405 both with and without reaction field. These results indicate that
406 there is no major benefit in choosing a longer cutoff radius in
407 simulations using SSD. This is advantageous in that the use of a
408 longer cutoff radius results in a significant increase in the time
409 required to obtain a single trajectory.
410
411 The key feature to recognize in figure \ref{dense1} is the density
412 scaling of SSD relative to other common models at any given
413 temperature. SSD assumes a lower density than any of the other listed
414 models at the same pressure, behavior which is especially apparent at
415 temperatures greater than 300 K. Lower than expected densities have
416 been observed for other systems using a reaction field for long-range
417 electrostatic interactions, so the most likely reason for the
418 significantly lower densities seen in these simulations is the
419 presence of the reaction field.\cite{Berendsen98,Nezbeda02} In order
420 to test the effect of the reaction field on the density of the
421 systems, the simulations were repeated without a reaction field
422 present. The results of these simulations are also displayed in figure
423 \ref{dense1}. Without the reaction field, the densities increase
424 to more experimentally reasonable values, especially around the
425 freezing point of liquid water. The shape of the curve is similar to
426 the curve produced from SSD simulations using reaction field,
427 specifically the rapidly decreasing densities at higher temperatures;
428 however, a shift in the density maximum location, down to 245 K, is
429 observed. This is a more accurate comparison to the other listed water
430 models, in that no long range corrections were applied in those
431 simulations.\cite{Clancy94,Jorgensen98b} However, even without the
432 reaction field, the density around 300 K is still significantly lower
433 than experiment and comparable water models. This anomalous behavior
434 was what lead Ichiye {\it et al.} to recently reparameterize
435 SSD.\cite{Ichiye03} Throughout the remainder of the paper our
436 reparamaterizations of SSD will be compared with the newer SSD1 model.
437
438 \subsection{Transport Behavior}
439
440 Accurate dynamical properties of a water model are particularly
441 important when using the model to study permeation or transport across
442 biological membranes. In order to probe transport in bulk water,
443 constant energy (NVE) simulations were performed at the average
444 density obtained by the NPT simulations at an identical target
445 temperature. Simulations started with randomized velocities and
446 underwent 50 ps of temperature scaling and 50 ps of constant energy
447 equilibration before a 200 ps data collection run. Diffusion constants
448 were calculated via linear fits to the long-time behavior of the
449 mean-square displacement as a function of time. The averaged results
450 from five sets of NVE simulations are displayed in figure
451 \ref{diffuse}, alongside experimental, SPC/E, and TIP5P
452 results.\cite{Gillen72,Mills73,Clancy94,Jorgensen01}
453
454 \begin{figure}
455 \begin{center}
456 \epsfxsize=6in
457 \epsfbox{betterDiffuse.epsi}
458 \caption{Average self-diffusion constant as a function of temperature for
459 SSD, SPC/E [Ref. \citen{Clancy94}], TIP5P [Ref. \citen{Jorgensen01}],
460 and Experimental data [Refs. \citen{Gillen72} and \citen{Mills73}]. Of
461 the three water models shown, SSD has the least deviation from the
462 experimental values. The rapidly increasing diffusion constants for
463 TIP5P and SSD correspond to significant decrease in density at the
464 higher temperatures.}
465 \label{diffuse}
466 \end{center}
467 \end{figure}
468
469 The observed values for the diffusion constant point out one of the
470 strengths of the SSD model. Of the three models shown, the SSD model
471 has the most accurate depiction of self-diffusion in both the
472 supercooled and liquid regimes. SPC/E does a respectable job by
473 reproducing values similar to experiment around 290 K; however, it
474 deviates at both higher and lower temperatures, failing to predict the
475 correct thermal trend. TIP5P and SSD both start off low at colder
476 temperatures and tend to diffuse too rapidly at higher temperatures.
477 This behavior at higher temperatures is not particularly surprising
478 since the densities of both TIP5P and SSD are lower than experimental
479 water densities at higher temperatures. When calculating the
480 diffusion coefficients for SSD at experimental densities (instead of
481 the densities from the NPT simulations), the resulting values fall
482 more in line with experiment at these temperatures.
483
484 \subsection{Structural Changes and Characterization}
485
486 By starting the simulations from the crystalline state, the melting
487 transition and the ice structure can be obtained along with the liquid
488 phase behavior beyond the melting point. The constant pressure heat
489 capacity (C$_\text{p}$) was monitored to locate the melting transition
490 in each of the simulations. In the melting simulations of the 1024
491 particle ice $I_h$ simulations, a large spike in C$_\text{p}$ occurs
492 at 245 K, indicating a first order phase transition for the melting of
493 these ice crystals. When the reaction field is turned off, the melting
494 transition occurs at 235 K. These melting transitions are
495 considerably lower than the experimental value.
496
497 \begin{figure}
498 \begin{center}
499 \epsfxsize=6in
500 \epsfbox{corrDiag.eps}
501 \caption{Two dimensional illustration of angles involved in the
502 correlations observed in Fig. \ref{contour}.}
503 \label{corrAngle}
504 \end{center}
505 \end{figure}
506
507 \begin{figure}
508 \begin{center}
509 \epsfxsize=6in
510 \epsfbox{fullContours.eps}
511 \caption{Contour plots of 2D angular g($r$)'s for 512 SSD systems at
512 100 K (A \& B) and 300 K (C \& D). Contour colors are inverted for
513 clarity: dark areas signify peaks while light areas signify
514 depressions. White areas have $g(r)$ values below 0.5 and black
515 areas have values above 1.5.}
516 \label{contour}
517 \end{center}
518 \end{figure}
519
520 Additional analysis of the melting process was performed using
521 two-dimensional structure and dipole angle correlations. Expressions
522 for these correlations are as follows:
523
524 \begin{equation}
525 g_{\text{AB}}(r,\cos\theta) = \frac{V}{N_\text{A}N_\text{B}}\langle\sum_{i\in\text{A}}\sum_{j\in\text{B}}\delta(\cos\theta-\cos\theta_{ij})\delta(r-\left|{\bf r}_{ij}\right|)\rangle\ ,
526 \end{equation}
527 \begin{equation}
528 g_{\text{AB}}(r,\cos\omega) =
529 \frac{V}{N_\text{A}N_\text{B}}\langle\sum_{i\in\text{A}}\sum_{j\in\text{B}}\delta(\cos\omega-\cos\omega_{ij})\delta(r-\left|{\bf r}_{ij}\right|)\rangle\ ,
530 \end{equation}
531 where $\theta$ and $\omega$ refer to the angles shown in figure
532 \ref{corrAngle}. By binning over both distance and the cosine of the
533 desired angle between the two dipoles, the $g(r)$ can be analyzed to
534 determine the common dipole arrangements that constitute the peaks and
535 troughs in the standard one-dimensional $g(r)$ plots. Frames A and B
536 of figure \ref{contour} show results from an ice $I_c$ simulation. The
537 first peak in the $g(r)$ consists primarily of the preferred hydrogen
538 bonding arrangements as dictated by the tetrahedral sticky potential -
539 one peak for the hydrogen bond donor and the other for the hydrogen
540 bond acceptor. Due to the high degree of crystallinity of the sample,
541 the second and third solvation shells show a repeated peak arrangement
542 which decays at distances around the fourth solvation shell, near the
543 imposed cutoff for the Lennard-Jones and dipole-dipole interactions.
544 In the higher temperature simulation shown in frames C and D, these
545 long-range features deteriorate rapidly. The first solvation shell
546 still shows the strong effect of the sticky-potential, although it
547 covers a larger area, extending to include a fraction of aligned
548 dipole peaks within the first solvation shell. The latter peaks lose
549 due to thermal motion and as the competing dipole force overcomes the
550 sticky potential's tight tetrahedral structuring of the crystal.
551
552 This complex interplay between dipole and sticky interactions was
553 remarked upon as a possible reason for the split second peak in the
554 oxygen-oxygen $g_\mathrm{OO}(r)$.\cite{Ichiye96} At low temperatures,
555 the second solvation shell peak appears to have two distinct
556 components that blend together to form one observable peak. At higher
557 temperatures, this split character alters to show the leading 4 \AA\
558 peak dominated by equatorial anti-parallel dipole orientations. There
559 is also a tightly bunched group of axially arranged dipoles that most
560 likely consist of the smaller fraction of aligned dipole pairs. The
561 trailing component of the split peak at 5 \AA\ is dominated by aligned
562 dipoles that assume hydrogen bond arrangements similar to those seen
563 in the first solvation shell. This evidence indicates that the dipole
564 pair interaction begins to dominate outside of the range of the
565 dipolar repulsion term. The energetically favorable dipole
566 arrangements populate the region immediately outside this repulsion
567 region (around 4 \AA), while arrangements that seek to satisfy both
568 the sticky and dipole forces locate themselves just beyond this
569 initial buildup (around 5 \AA).
570
571 From these findings, the split second peak is primarily the product of
572 the dipolar repulsion term of the sticky potential. In fact, the inner
573 peak can be pushed out and merged with the outer split peak just by
574 extending the switching function ($s^\prime(r_{ij})$) from its normal
575 4.0 \AA\ cutoff to values of 4.5 or even 5 \AA. This type of
576 correction is not recommended for improving the liquid structure,
577 since the second solvation shell would still be shifted too far
578 out. In addition, this would have an even more detrimental effect on
579 the system densities, leading to a liquid with a more open structure
580 and a density considerably lower than the already low SSD density. A
581 better correction would be to include the quadrupole-quadrupole
582 interactions for the water particles outside of the first solvation
583 shell, but this would remove the simplicity and speed advantage of
584 SSD.
585
586 \subsection{Adjusted Potentials: SSD/RF and SSD/E}
587
588 The propensity of SSD to adopt lower than expected densities under
589 varying conditions is troubling, especially at higher temperatures. In
590 order to correct this model for use with a reaction field, it is
591 necessary to adjust the force field parameters for the primary
592 intermolecular interactions. In undergoing a reparameterization, it is
593 important not to focus on just one property and neglect the other
594 important properties. In this case, it would be ideal to correct the
595 densities while maintaining the accurate transport behavior.
596
597 The parameters available for tuning include the $\sigma$ and
598 $\epsilon$ Lennard-Jones parameters, the dipole strength ($\mu$), the
599 strength of the sticky potential ($\nu_0$), and the sticky attractive
600 and dipole repulsive cubic switching function cutoffs ($r_l$, $r_u$
601 and $r_l^\prime$, $r_u^\prime$ respectively). The results of the
602 reparameterizations are shown in table \ref{params}. We are calling
603 these reparameterizations the Soft Sticky Dipole / Reaction Field
604 (SSD/RF - for use with a reaction field) and Soft Sticky Dipole
605 Extended (SSD/E - an attempt to improve the liquid structure in
606 simulations without a long-range correction).
607
608 \begin{table}
609 \begin{center}
610 \caption{Parameters for the original and adjusted models}
611 \begin{tabular}{ l c c c c }
612 \hline \\[-3mm]
613 \ \ \ Parameters\ \ \ & \ \ \ SSD [Ref. \citen{Ichiye96}] \ \ \
614 & \ SSD1 [Ref. \citen{Ichiye03}]\ \ & \ SSD/E\ \ & \ SSD/RF \\
615 \hline \\[-3mm]
616 \ \ \ $\sigma$ (\AA) & 3.051 & 3.016 & 3.035 & 3.019\\
617 \ \ \ $\epsilon$ (kcal/mol) & 0.152 & 0.152 & 0.152 & 0.152\\
618 \ \ \ $\mu$ (D) & 2.35 & 2.35 & 2.42 & 2.48\\
619 \ \ \ $\nu_0$ (kcal/mol) & 3.7284 & 3.6613 & 3.90 & 3.90\\
620 \ \ \ $\omega^\circ$ & 0.07715 & 0.07715 & 0.07715 & 0.07715\\
621 \ \ \ $r_l$ (\AA) & 2.75 & 2.75 & 2.40 & 2.40\\
622 \ \ \ $r_u$ (\AA) & 3.35 & 3.35 & 3.80 & 3.80\\
623 \ \ \ $r_l^\prime$ (\AA) & 2.75 & 2.75 & 2.75 & 2.75\\
624 \ \ \ $r_u^\prime$ (\AA) & 4.00 & 4.00 & 3.35 & 3.35\\
625 \end{tabular}
626 \label{params}
627 \end{center}
628 \end{table}
629
630 \begin{figure}
631 \begin{center}
632 \epsfxsize=5in
633 \epsfbox{GofRCompare.epsi}
634 \caption{Plots comparing experiment [Ref. \citen{Head-Gordon00_1}] with SSD/E
635 and SSD1 without reaction field (top), as well as SSD/RF and SSD1 with
636 reaction field turned on (bottom). The insets show the respective
637 first peaks in detail. Note how the changes in parameters have lowered
638 and broadened the first peak of SSD/E and SSD/RF.}
639 \label{grcompare}
640 \end{center}
641 \end{figure}
642
643 \begin{figure}
644 \begin{center}
645 \epsfxsize=6in
646 \epsfbox{dualsticky.ps}
647 \caption{Isosurfaces of the sticky potential for SSD1 (left) and SSD/E \&
648 SSD/RF (right). Light areas correspond to the tetrahedral attractive
649 component, and darker areas correspond to the dipolar repulsive
650 component.}
651 \label{isosurface}
652 \end{center}
653 \end{figure}
654
655 In the original paper detailing the development of SSD, Liu and Ichiye
656 placed particular emphasis on an accurate description of the first
657 solvation shell. This resulted in a somewhat tall and narrow first
658 peak in $g(r)$ that integrated to give similar coordination numbers to
659 the experimental data obtained by Soper and
660 Phillips.\cite{Ichiye96,Soper86} New experimental x-ray scattering
661 data from the Head-Gordon lab indicates a slightly lower and shifted
662 first peak in the g$_\mathrm{OO}(r)$, so our adjustments to SSD were
663 made while taking into consideration the new experimental
664 findings.\cite{Head-Gordon00_1} Figure \ref{grcompare} shows the
665 relocation of the first peak of the oxygen-oxygen $g(r)$ by comparing
666 the revised SSD model (SSD1), SSD/E, and SSD/RF to the new
667 experimental results. Both modified water models have shorter peaks
668 that match more closely to the experimental peak (as seen in the
669 insets of figure \ref{grcompare}). This structural alteration was
670 accomplished by the combined reduction in the Lennard-Jones $\sigma$
671 variable and adjustment of the sticky potential strength and cutoffs.
672 As can be seen in table \ref{params}, the cutoffs for the tetrahedral
673 attractive and dipolar repulsive terms were nearly swapped with each
674 other. Isosurfaces of the original and modified sticky potentials are
675 shown in figure \ref{isosurface}. In these isosurfaces, it is easy to
676 see how altering the cutoffs changes the repulsive and attractive
677 character of the particles. With a reduced repulsive surface (darker
678 region), the particles can move closer to one another, increasing the
679 density for the overall system. This change in interaction cutoff also
680 results in a more gradual orientational motion by allowing the
681 particles to maintain preferred dipolar arrangements before they begin
682 to feel the pull of the tetrahedral restructuring. As the particles
683 move closer together, the dipolar repulsion term becomes active and
684 excludes unphysical nearest-neighbor arrangements. This compares with
685 how SSD and SSD1 exclude preferred dipole alignments before the
686 particles feel the pull of the ``hydrogen bonds''. Aside from
687 improving the shape of the first peak in the g(\emph{r}), this
688 modification improves the densities considerably by allowing the
689 persistence of full dipolar character below the previous 4.0 \AA\
690 cutoff.
691
692 While adjusting the location and shape of the first peak of $g(r)$
693 improves the densities, these changes alone are insufficient to bring
694 the system densities up to the values observed experimentally. To
695 further increase the densities, the dipole moments were increased in
696 both of our adjusted models. Since SSD is a dipole based model, the
697 structure and transport are very sensitive to changes in the dipole
698 moment. The original SSD simply used the dipole moment calculated from
699 the TIP3P water model, which at 2.35 D is significantly greater than
700 the experimental gas phase value of 1.84 D. The larger dipole moment
701 is a more realistic value and improves the dielectric properties of
702 the fluid. Both theoretical and experimental measurements indicate a
703 liquid phase dipole moment ranging from 2.4 D to values as high as
704 3.11 D, providing a substantial range of reasonable values for a
705 dipole moment.\cite{Sprik91,Kusalik02,Badyal00,Barriol64} Moderately
706 increasing the dipole moments to 2.42 and 2.48 D for SSD/E and SSD/RF,
707 respectively, leads to significant changes in the density and
708 transport of the water models.
709
710 In order to demonstrate the benefits of these reparameterizations, a
711 series of NPT and NVE simulations were performed to probe the density
712 and transport properties of the adapted models and compare the results
713 to the original SSD model. This comparison involved full NPT melting
714 sequences for both SSD/E and SSD/RF, as well as NVE transport
715 calculations at the calculated self-consistent densities. Again, the
716 results are obtained from five separate simulations of 1024 particle
717 systems, and the melting sequences were started from different ice
718 $I_h$ crystals constructed as described previously. Each NPT
719 simulation was equilibrated for 100 ps before a 200 ps data collection
720 run at each temperature step, and the final configuration from the
721 previous temperature simulation was used as a starting point. All NVE
722 simulations had the same thermalization, equilibration, and data
723 collection times as stated previously.
724
725 \begin{figure}
726 \begin{center}
727 \epsfxsize=6in
728 \epsfbox{ssdeDense.epsi}
729 \caption{Comparison of densities calculated with SSD/E to SSD1 without a
730 reaction field, TIP3P [Ref. \citen{Jorgensen98b}], TIP5P
731 [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}] and
732 experiment [Ref. \citen{CRC80}]. The window shows a expansion around
733 300 K with error bars included to clarify this region of
734 interest. Note that both SSD1 and SSD/E show good agreement with
735 experiment when the long-range correction is neglected.}
736 \label{ssdedense}
737 \end{center}
738 \end{figure}
739
740 Fig. \ref{ssdedense} shows the density profile for the SSD/E model
741 in comparison to SSD1 without a reaction field, other common water
742 models, and experimental results. The calculated densities for both
743 SSD/E and SSD1 have increased significantly over the original SSD
744 model (see fig. \ref{dense1}) and are in better agreement with the
745 experimental values. At 298 K, the densities of SSD/E and SSD1 without
746 a long-range correction are 0.996$\pm$0.001 g/cm$^3$ and
747 0.999$\pm$0.001 g/cm$^3$ respectively. These both compare well with
748 the experimental value of 0.997 g/cm$^3$, and they are considerably
749 better than the SSD value of 0.967$\pm$0.003 g/cm$^3$. The changes to
750 the dipole moment and sticky switching functions have improved the
751 structuring of the liquid (as seen in figure \ref{grcompare}, but they
752 have shifted the density maximum to much lower temperatures. This
753 comes about via an increase in the liquid disorder through the
754 weakening of the sticky potential and strengthening of the dipolar
755 character. However, this increasing disorder in the SSD/E model has
756 little effect on the melting transition. By monitoring $C_p$
757 throughout these simulations, the melting transition for SSD/E was
758 shown to occur at 235 K. The same transition temperature observed
759 with SSD and SSD1.
760
761 \begin{figure}
762 \begin{center}
763 \epsfxsize=6in
764 \epsfbox{ssdrfDense.epsi}
765 \caption{Comparison of densities calculated with SSD/RF to SSD1 with a
766 reaction field, TIP3P [Ref. \citen{Jorgensen98b}], TIP5P
767 [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}], and
768 experiment [Ref. \citen{CRC80}]. The inset shows the necessity of
769 reparameterization when utilizing a reaction field long-ranged
770 correction - SSD/RF provides significantly more accurate densities
771 than SSD1 when performing room temperature simulations.}
772 \label{ssdrfdense}
773 \end{center}
774 \end{figure}
775
776 Including the reaction field long-range correction in the simulations
777 results in a more interesting comparison. A density profile including
778 SSD/RF and SSD1 with an active reaction field is shown in figure
779 \ref{ssdrfdense}. As observed in the simulations without a reaction
780 field, the densities of SSD/RF and SSD1 show a dramatic increase over
781 normal SSD (see figure \ref{dense1}). At 298 K, SSD/RF has a density
782 of 0.997$\pm$0.001 g/cm$^3$, directly in line with experiment and
783 considerably better than the original SSD value of 0.941$\pm$0.001
784 g/cm$^3$ and the SSD1 value of 0.972$\pm$0.002 g/cm$^3$. These results
785 further emphasize the importance of reparameterization in order to
786 model the density properly under different simulation conditions.
787 Again, these changes have only a minor effect on the melting point,
788 which observed at 245 K for SSD/RF, is identical to SSD and only 5 K
789 lower than SSD1 with a reaction field. Additionally, the difference in
790 density maxima is not as extreme, with SSD/RF showing a density
791 maximum at 255 K, fairly close to the density maxima of 260 K and 265
792 K, shown by SSD and SSD1 respectively.
793
794 \begin{figure}
795 \begin{center}
796 \epsfxsize=6in
797 \epsfbox{ssdeDiffuse.epsi}
798 \caption{The diffusion constants calculated from SSD/E and SSD1,
799 both without a reaction field, along with experimental results
800 [Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations
801 were performed at the average densities observed in the 1 atm NPT
802 simulations for the respective models. SSD/E is slightly more mobile
803 than experiment at all of the temperatures, but it is closer to
804 experiment at biologically relavent temperatures than SSD1 without a
805 long-range correction.}
806 \label{ssdediffuse}
807 \end{center}
808 \end{figure}
809
810 The reparameterization of the SSD water model, both for use with and
811 without an applied long-range correction, brought the densities up to
812 what is expected for simulating liquid water. In addition to improving
813 the densities, it is important that the excellent diffusive behavior
814 of SSD be maintained or improved. Figure \ref{ssdediffuse} compares
815 the temperature dependence of the diffusion constant of SSD/E to SSD1
816 without an active reaction field at the densities calculated from the
817 NPT simulations at 1 atm. The diffusion constant for SSD/E is
818 consistently higher than experiment, while SSD1 remains lower than
819 experiment until relatively high temperatures (around 360 K). Both
820 models follow the shape of the experimental curve well below 300 K but
821 tend to diffuse too rapidly at higher temperatures, as seen in SSD1's
822 crossing above 360 K. This increasing diffusion relative to the
823 experimental values is caused by the rapidly decreasing system density
824 with increasing temperature. Both SSD1 and SSD/E show this deviation
825 in diffusive behavior, but this trend has different implications on
826 the diffusive behavior of the models. While SSD1 shows more
827 experimentally accurate diffusive behavior in the high temperature
828 regimes, SSD/E shows more accurate behavior in the supercooled and
829 biologically relavent temperature ranges. Thus, the changes made to
830 improve the liquid structure may have had an adverse affect on the
831 density maximum, but they improve the transport behavior of SSD/E
832 relative to SSD1 under the most commonly simulated conditions.
833
834 \begin{figure}
835 \begin{center}
836 \epsfxsize=6in
837 \epsfbox{ssdrfDiffuse.epsi}
838 \caption{The diffusion constants calculated from SSD/RF and SSD1,
839 both with an active reaction field, along with experimental results
840 [Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations
841 were performed at the average densities observed in the 1 atm NPT
842 simulations for both of the models. Note how accurately SSD/RF
843 simulates the diffusion of water throughout this temperature
844 range. The more rapidly increasing diffusion constants at high
845 temperatures for both models is attributed to lower calculated
846 densities than those observed in experiment.}
847 \label{ssdrfdiffuse}
848 \end{center}
849 \end{figure}
850
851 In figure \ref{ssdrfdiffuse}, the diffusion constants for SSD/RF are
852 compared to SSD1 with an active reaction field. Note that SSD/RF
853 tracks the experimental results quantitatively, identical within error
854 throughout most of the temperature range shown and exhibiting only a
855 slight increasing trend at higher temperatures. SSD1 tends to diffuse
856 more slowly at low temperatures and deviates to diffuse too rapidly at
857 temperatures greater than 330 K. As stated above, this deviation away
858 from the ideal trend is due to a rapid decrease in density at higher
859 temperatures. SSD/RF does not suffer from this problem as much as SSD1
860 because the calculated densities are closer to the experimental
861 values. These results again emphasize the importance of careful
862 reparameterization when using an altered long-range correction.
863
864 \begin{table}
865 \begin{center}
866 \caption{Calculated and experimental properties of the single point waters and liquid water at 298 K and 1 atm. (a) Ref. [\citen{Mills73}]. (b) Calculated by integrating the data in ref. \citen{Head-Gordon00_1}. (c) Calculated by integrating the data in ref. \citen{Soper86}. (d) Ref. [\citen{Eisenberg69}]. (e) Calculated for 298 K from data in ref. \citen{Krynicki66}.}
867 \begin{tabular}{ l c c c c c }
868 \hline \\[-3mm]
869 \ \ \ \ \ \ & \ \ \ SSD1 \ \ \ & \ SSD/E \ \ \ & \ SSD1 (RF) \ \
870 \ & \ SSD/RF \ \ \ & \ Expt. \\
871 \hline \\[-3mm]
872 \ \ \ $\rho$ (g/cm$^3$) & 0.999 $\pm$0.001 & 0.996 $\pm$0.001 & 0.972 $\pm$0.002 & 0.997 $\pm$0.001 & 0.997 \\
873 \ \ \ $C_p$ (cal/mol K) & 28.80 $\pm$0.11 & 25.45 $\pm$0.09 & 28.28 $\pm$0.06 & 23.83 $\pm$0.16 & 17.98 \\
874 \ \ \ $D$ ($10^{-5}$ cm$^2$/s) & 1.78 $\pm$0.07 & 2.51 $\pm$0.18 & 2.00 $\pm$0.17 & 2.32 $\pm$0.06 & 2.299$^\text{a}$ \\
875 \ \ \ Coordination Number & 3.9 & 4.3 & 3.8 & 4.4 & 4.7$^\text{b}$ \\
876 \ \ \ H-bonds per particle & 3.7 & 3.6 & 3.7 & 3.7 & 3.4$^\text{c}$ \\
877 \ \ \ $\tau_1^\mu$ (ps) & 10.9 $\pm$0.6 & 7.3 $\pm$0.4 & 7.5 $\pm$0.7 & 7.2 $\pm$0.4 & 4.76$^\text{d}$ \\
878 \ \ \ $\tau_2^\mu$ (ps) & 4.7 $\pm$0.4 & 3.1 $\pm$0.2 & 3.5 $\pm$0.3 & 3.2 $\pm$0.2 & 2.3$^\text{e}$ \\
879 \end{tabular}
880 \label{liquidproperties}
881 \end{center}
882 \end{table}
883
884 Table \ref{liquidproperties} gives a synopsis of the liquid state
885 properties of the water models compared in this study along with the
886 experimental values for liquid water at ambient conditions. The
887 coordination number and hydrogen bonds per particle were calculated by
888 integrating the following relation:
889 \begin{equation}
890 4\pi\rho\int_{0}^{a}r^2\text{g}(r)dr,
891 \end{equation}
892 where $\rho$ is the number density of pair interactions, $a$ is the
893 radial location of the minima following the first solvation shell
894 peak, and g$(r)$ is either g$_\text{OO}(r)$ or g$_\text{OH}(r)$ for
895 calculation of the coordination number or hydrogen bonds per particle
896 respectively. The number of hydrogen bonds stays relatively constant
897 across all of the models, but the coordination numbers of SSD/E and
898 SSD/RF show an improvement over SSD1. This improvement is primarily
899 due to the widening of the first solvation shell peak, allowing the
900 first minima to push outward. Comparing the coordination number with
901 the number of hydrogen bonds can lead to more insight into the
902 structural character of the liquid. Because of the near identical
903 values for SSD1, it appears to be a little too exclusive, in that all
904 molecules in the first solvation shell are involved in forming ideal
905 hydrogen bonds. The differing numbers for the newly parameterized
906 models indicate the allowance of more fluid configurations in addition
907 to the formation of an acceptable number of ideal hydrogen bonds.
908
909 The time constants for the self orientational autocorrelation function
910 are also displayed in Table \ref{liquidproperties}. The dipolar
911 orientational time correlation function ($\Gamma_{l}$) is described
912 by:
913 \begin{equation}
914 \Gamma_{l}(t) = \langle P_l[\mathbf{u}_j(0)\cdot\mathbf{u}_j(t)]\rangle,
915 \end{equation}
916 where $P_l$ is a Legendre polynomial of order $l$ and $\mathbf{u}_j$
917 is the unit vector of the particle dipole.\cite{Rahman71} From these
918 correlation functions, the orientational relaxation time of the dipole
919 vector can be calculated from an exponential fit in the long-time
920 regime ($t > \tau_l^\mu$).\cite{Rothschild84} Calculation of these
921 time constants were averaged from five detailed NVE simulations
922 performed at the STP density for each of the respective models. Again,
923 SSD/E and SSD/RF show improved behavior over SSD1 both with and
924 without an active reaction field. Numbers published from the original
925 SSD dynamics studies appear closer to the experimental values, and we
926 attribute this discrepancy to the implimentation of an Ewald sum
927 versus a reaction field.
928
929 \subsection{Additional Observations}
930
931 \begin{figure}
932 \begin{center}
933 \epsfxsize=6in
934 \epsfbox{povIce.ps}
935 \caption{A water lattice built from the crystal structure assumed by
936 SSD/E when undergoing an extremely restricted temperature NPT
937 simulation. This form of ice is referred to as ice-{\it i} to
938 emphasize its simulation origins. This image was taken of the (001)
939 face of the crystal.}
940 \label{weirdice}
941 \end{center}
942 \end{figure}
943
944 While performing a series of melting simulations on an early iteration
945 of SSD/E not discussed in this paper, we observed recrystallization
946 into a novel structure not previously known for water. After melting
947 at 235 K, two of five systems underwent crystallization events near
948 245 K. The two systems remained crystalline up to 320 and 330 K,
949 respectively. The crystal exhibits an expanded zeolite-like structure
950 that does not correspond to any known form of ice. This appears to be
951 an artifact of the point dipolar models, so to distinguish it from the
952 experimentally observed forms of ice, we have denoted the structure
953 Ice-$\sqrt{\smash[b]{-\text{I}}}$ (ice-{\it i}). A large enough
954 portion of the sample crystallized that we have been able to obtain a
955 near ideal crystal structure of ice-{\it i}. Figure \ref{weirdice}
956 shows the repeating crystal structure of a typical crystal at 5
957 K. Each water molecule is hydrogen bonded to four others; however, the
958 hydrogen bonds are bent rather than perfectly straight. This results
959 in a skewed tetrahedral geometry about the central molecule. In
960 figure \ref{isosurface}, it is apparent that these flexed hydrogen
961 bonds are allowed due to the conical shape of the attractive regions,
962 with the greatest attraction along the direct hydrogen bond
963 configuration. Though not ideal, these flexed hydrogen bonds are
964 favorable enough to stabilize an entire crystal generated around them.
965
966 Initial simulations indicated that ice-{\it i} is the preferred ice
967 structure for at least the SSD/E model. To verify this, a comparison
968 was made between near ideal crystals of ice~$I_h$, ice~$I_c$, and
969 ice-{\it i} at constant pressure with SSD/E, SSD/RF, and
970 SSD1. Near-ideal versions of the three types of crystals were cooled
971 to 1 K, and the enthalpies of each were compared using all three water
972 models. With every model in the SSD family, ice-{\it i} had the lowest
973 calculated enthalpy: 5\% lower than $I_h$ with SSD1, 6.5\% lower with
974 SSD/E, and 7.5\% lower with SSD/RF. The enthalpy data is summarized
975 in Table \ref{iceenthalpy}.
976
977 \begin{table}
978 \begin{center}
979 \caption{Enthalpies (in kcal / mol) of the three crystal structures (at 1
980 K) exhibited by the SSD family of water models}
981 \begin{tabular}{ l c c c }
982 \hline \\[-3mm]
983 \ \ \ Water Model \ \ \ & \ \ \ Ice-$I_h$ \ \ \ & \ Ice-$I_c$\ \ & \
984 Ice-{\it i} \\
985 \hline \\[-3mm]
986 \ \ \ SSD/E & -12.286 & -12.292 & -13.590 \\
987 \ \ \ SSD/RF & -12.935 & -12.917 & -14.022 \\
988 \ \ \ SSD1 & -12.496 & -12.411 & -13.417 \\
989 \ \ \ SSD1 (RF) & -12.504 & -12.411 & -13.134 \\
990 \end{tabular}
991 \label{iceenthalpy}
992 \end{center}
993 \end{table}
994
995 In addition to these energetic comparisons, melting simulations were
996 performed with ice-{\it i} as the initial configuration using SSD/E,
997 SSD/RF, and SSD1 both with and without a reaction field. The melting
998 transitions for both SSD/E and SSD1 without reaction field occurred at
999 temperature in excess of 375~K. SSD/RF and SSD1 with a reaction field
1000 showed more reasonable melting transitions near 325~K. These melting
1001 point observations clearly show that all of the SSD-derived models
1002 prefer the ice-{\it i} structure.
1003
1004 \section{Conclusions}
1005
1006 The density maximum and temperature dependence of the self-diffusion
1007 constant were studied for the SSD water model, both with and without
1008 the use of reaction field, via a series of NPT and NVE
1009 simulations. The constant pressure simulations showed a density
1010 maximum near 260 K. In most cases, the calculated densities were
1011 significantly lower than the densities obtained from other water
1012 models (and experiment). Analysis of self-diffusion showed SSD to
1013 capture the transport properties of water well in both the liquid and
1014 super-cooled liquid regimes.
1015
1016 In order to correct the density behavior, the original SSD model was
1017 reparameterized for use both with and without a reaction field (SSD/RF
1018 and SSD/E), and comparisons were made with SSD1, Ichiye's density
1019 corrected version of SSD. Both models improve the liquid structure,
1020 densities, and diffusive properties under their respective simulation
1021 conditions, indicating the necessity of reparameterization when
1022 changing the method of calculating long-range electrostatic
1023 interactions. In general, however, these simple water models are
1024 excellent choices for representing explicit water in large scale
1025 simulations of biochemical systems.
1026
1027 The existence of a novel low-density ice structure that is preferred
1028 by the SSD family of water models is somewhat troubling, since liquid
1029 simulations on this family of water models at room temperature are
1030 effectively simulations of super-cooled or metastable liquids. One
1031 way to de-stabilize this unphysical ice structure would be to make the
1032 range of angles preferred by the attractive part of the sticky
1033 potential much narrower. This would require extensive
1034 reparameterization to maintain the same level of agreement with the
1035 experiments.
1036
1037 Additionally, our initial calculations show that the ice-{\it i}
1038 structure may also be a preferred crystal structure for at least one
1039 other popular multi-point water model (TIP3P), and that much of the
1040 simulation work being done using this popular model could also be at
1041 risk for crystallization into this unphysical structure. A future
1042 publication will detail the relative stability of the known ice
1043 structures for a wide range of popular water models.
1044
1045 \section{Acknowledgments}
1046 Support for this project was provided by the National Science
1047 Foundation under grant CHE-0134881. Computation time was provided by
1048 the Notre Dame Bunch-of-Boxes (B.o.B) computer cluster under NSF grant
1049 DMR-0079647.
1050
1051 \newpage
1052
1053 \bibliographystyle{jcp}
1054 \bibliography{nptSSD}
1055
1056 %\pagebreak
1057
1058 \end{document}