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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
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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
94 was 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
97 which 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 shell.
103
104 The interaction between two SSD water molecules \emph{i} and \emph{j}
105 is given by the potential
106 \begin{equation}
107 u_{ij} = u_{ij}^{LJ} (r_{ij})\ + u_{ij}^{dp}
108 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)\ +
109 u_{ij}^{sp}
110 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j),
111 \end{equation}
112 where the ${\bf r}_{ij}$ is the position vector between molecules
113 \emph{i} and \emph{j} with magnitude $r_{ij}$, and
114 ${\bf \Omega}_i$ and ${\bf \Omega}_j$ represent the orientations of
115 the two molecules. The Lennard-Jones and dipole interactions are given
116 by the following familiar forms:
117 \begin{equation}
118 u_{ij}^{LJ}(r_{ij}) = 4\epsilon
119 \left[\left(\frac{\sigma}{r_{ij}}\right)^{12}-\left(\frac{\sigma}{r_{ij}}\right)^{6}\right]
120 \ ,
121 \end{equation}
122 and
123 \begin{equation}
124 u_{ij}^{dp} = \frac{|\mu_i||\mu_j|}{4 \pi \epsilon_0 r_{ij}^3} \left(
125 \hat{\bf u}_i \cdot \hat{\bf u}_j - 3(\hat{\bf u}_i\cdot\hat{\bf
126 r}_{ij})(\hat{\bf u}_j\cdot\hat{\bf r}_{ij}) \right)\ ,
127 \end{equation}
128 where $\hat{\bf u}_i$ and $\hat{\bf u}_j$ are the unit vectors along
129 the dipoles of molecules $i$ and $j$ respectively. $|\mu_i|$ and
130 $|\mu_j|$ are the strengths of the dipole moments, and $\hat{\bf
131 r}_{ij}$ is the unit vector pointing from molecule $j$ to molecule
132 $i$.
133
134 The sticky potential is somewhat less familiar:
135 \begin{equation}
136 u_{ij}^{sp}
137 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j) =
138 \frac{\nu_0}{2}[s(r_{ij})w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)
139 + s^\prime(r_{ij})w^\prime({\bf r}_{ij},{\bf \Omega}_i,{\bf
140 \Omega}_j)]\ .
141 \label{stickyfunction}
142 \end{equation}
143 Here, $\nu_0$ is a strength parameter for the sticky potential, and
144 $s$ and $s^\prime$ are cubic switching functions which turn off the
145 sticky interaction beyond the first solvation shell. The $w$ function
146 can be thought of as an attractive potential with tetrahedral
147 geometry:
148 \begin{equation}
149 w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)=\sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij},
150 \end{equation}
151 while the $w^\prime$ function counters the normal aligned and
152 anti-aligned structures favored by point dipoles:
153 \begin{equation}
154 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,
155 \end{equation}
156 It should be noted that $w$ is proportional to the sum of the $Y_3^2$
157 and $Y_3^{-2}$ spherical harmonics (a linear combination which
158 enhances the tetrahedral geometry for hydrogen bonded structures),
159 while $w^\prime$ is a purely empirical function. A more detailed
160 description of the functional parts and variables in this potential
161 can be found in the original SSD
162 articles.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03}
163
164 Since SSD is a single-point {\it dipolar} model, the force
165 calculations are simplified significantly relative to the standard
166 {\it charged} multi-point models. In the original Monte Carlo
167 simulations using this model, Ichiye {\it et al.} reported that using
168 SSD decreased computer time by a factor of 6-7 compared to other
169 models.\cite{Ichiye96} What is most impressive is that this savings
170 did not come at the expense of accurate depiction of the liquid state
171 properties. Indeed, SSD maintains reasonable agreement with the
172 Soper data for the structural features of liquid
173 water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties
174 exhibited by SSD agree with experiment better than those of more
175 computationally expensive models (like TIP3P and
176 SPC/E).\cite{Ichiye99} The combination of speed and accurate depiction
177 of solvent properties makes SSD a very attractive model for the
178 simulation of large scale biochemical simulations.
179
180 One feature of the SSD model is that it was parameterized for
181 use with the Ewald sum to handle long-range interactions. This would
182 normally be the best way of handling long-range interactions in
183 systems that contain other point charges. However, our group has
184 recently become interested in systems with point dipoles as mimics for
185 neutral, but polarized regions on molecules (e.g. the zwitterionic
186 head group regions of phospholipids). If the system of interest does
187 not contain point charges, the Ewald sum and even particle-mesh Ewald
188 become computational bottlenecks. Their respective ideal
189 $N^\frac{3}{2}$ and $N\log N$ calculation scaling orders for $N$
190 particles can become prohibitive when $N$ becomes
191 large.\cite{Darden99} In applying this water model in these types of
192 systems, it would be useful to know its properties and behavior under
193 the more computationally efficient reaction field (RF) technique, or
194 even with a simple cutoff. This study addresses these issues by
195 looking at the structural and transport behavior of SSD over a
196 variety of temperatures with the purpose of utilizing the RF
197 correction technique. We then suggest modifications to the parameters
198 that result in more realistic bulk phase behavior. It should be noted
199 that in a recent publication, some of the original investigators of
200 the SSD water model have suggested adjustments to the SSD
201 water model to address abnormal density behavior (also observed here),
202 calling the corrected model SSD1.\cite{Ichiye03} In what
203 follows, we compare our reparamaterization of SSD with both the
204 original SSD and SSD1 models with the goal of improving
205 the bulk phase behavior of an SSD-derived model in simulations
206 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} s(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 $s(r_{ij})$ 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
240 field turned on.
241
242 Simulations to obtain the preferred densities of the models were
243 performed in the isobaric-isothermal (NPT) ensemble, while all
244 dynamical properties were obtained from microcanonical (NVE)
245 simulations done at densities matching the NPT density for a
246 particular target temperature. The constant pressure simulations were
247 implemented using an integral thermostat and barostat as outlined by
248 Hoover.\cite{Hoover85,Hoover86} All molecules were treated as
249 non-linear rigid bodies. Vibrational constraints are not necessary in
250 simulations of SSD, because there are no explicit hydrogen
251 atoms, and thus no molecular vibrational modes need to be considered.
252
253 Integration of the equations of motion was carried out using the
254 symplectic splitting method proposed by Dullweber, Leimkuhler, and
255 McLachlan ({\sc dlm}).\cite{Dullweber1997} Our reason for selecting
256 this integrator centers on poor energy conservation of rigid body
257 dynamics using traditional quaternion
258 integration.\cite{Evans77,Evans77b} In typical microcanonical ensemble
259 simulations, the energy drift when using quaternions was substantially
260 greater than when using the {\sc dlm} method (fig. \ref{timestep}).
261 This steady drift in the total energy has also been observed by Kol
262 {\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 {\sc dlm} method allows for Verlet style integration of both
272 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\%
278 increase in computation time using the {\sc dlm} 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 {\sc dlm} than would be usable under quaternion dynamics. The
282 energy conservation of the two methods using a number of different
283 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 {\sc dlm} method with increasing time step. The larger time step plots
292 are shifted from the true energy baseline (that of $\Delta t$ = 0.1
293 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 {\sc dlm} and quaternion integration schemes is
300 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 {\sc dlm} method are
307 clearly demonstrated. Thus, while maintaining the same degree of
308 energy conservation, one can take considerably longer time steps,
309 leading to an overall reduction in computation time.
310
311 Energy drift in the simulations using {\sc dlm} integration was
312 unnoticeable for 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 with
315 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
322 SSD particles into a ``hexagonal'' ice lattice of 1024
323 particles. Because of the crystal structure of $I_h$ ice, the
324 simulation box assumed an orthorhombic shape with an edge length ratio
325 of approximately 1.00$\times$1.06$\times$1.23. The particles were then
326 allowed to orient freely about fixed positions with angular momenta
327 randomized at 400 K for varying times. The rotational temperature was
328 then scaled down in stages to slowly cool the crystals to 25 K. The
329 particles were then allowed to translate with fixed orientations at a
330 constant pressure of 1 atm for 50 ps at 25 K. Finally, all constraints
331 were removed and the ice crystals were allowed to equilibrate for 50
332 ps at 25 K and a constant pressure of 1 atm. This procedure resulted
333 in 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,
361 and 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{denseSSDnew.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
387 simple water models. Figure \ref{dense1} also shows calculated
388 densities of 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
391 observed 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 to
394 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
402 simulations, all performed with a cutoff of 9.0 \AA. All of the
403 resulting densities overlapped within error and showed no significant
404 trend toward lower or higher densities as a function of cutoff radius,
405 for simulations both with and without reaction field. These results
406 indicate that there is no major benefit in choosing a longer cutoff
407 radius in simulations using SSD. This is advantageous in that
408 the use of a longer cutoff radius results in a significant increase in
409 the time 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
414 listed models at the same pressure, behavior which is especially
415 apparent at temperatures greater than 300 K. Lower than expected
416 densities have been observed for other systems using a reaction field
417 for long-range electrostatic interactions, so the most likely reason
418 for the 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 Tan {\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 their newer SSD1
437 model.
438
439 \subsection{Transport Behavior}
440
441 Accurate dynamical properties of a water model are particularly
442 important when using the model to study permeation or transport across
443 biological membranes. In order to probe transport in bulk water,
444 constant energy (NVE) simulations were performed at the average
445 density obtained by the NPT simulations at an identical target
446 temperature. Simulations started with randomized velocities and
447 underwent 50 ps of temperature scaling and 50 ps of constant energy
448 equilibration before a 200 ps data collection run. Diffusion constants
449 were calculated via linear fits to the long-time behavior of the
450 mean-square displacement as a function of time. The averaged results
451 from five sets of NVE simulations are displayed in figure
452 \ref{diffuse}, alongside experimental, SPC/E, and TIP5P
453 results.\cite{Gillen72,Holz00,Clancy94,Jorgensen01}
454
455 \begin{figure}
456 \begin{center}
457 \epsfxsize=6in
458 \epsfbox{betterDiffuse.epsi}
459 \caption{Average self-diffusion constant as a function of temperature for
460 SSD, SPC/E [Ref. \citen{Clancy94}], and TIP5P
461 [Ref. \citen{Jorgensen01}] compared with experimental data
462 [Refs. \citen{Gillen72} and \citen{Holz00}]. Of the three water models
463 shown, SSD has the least deviation from the experimental values. The
464 rapidly increasing diffusion constants for TIP5P and SSD correspond to
465 significant decreases in density at the higher temperatures.}
466 \label{diffuse}
467 \end{center}
468 \end{figure}
469
470 The observed values for the diffusion constant point out one of the
471 strengths of the SSD model. Of the three models shown, the SSD model
472 has the most accurate depiction of self-diffusion in both the
473 supercooled and liquid regimes. SPC/E does a respectable job by
474 reproducing values similar to experiment around 290 K; however, it
475 deviates at both higher and lower temperatures, failing to predict the
476 correct thermal trend. TIP5P and SSD both start off low at colder
477 temperatures and tend to diffuse too rapidly at higher temperatures.
478 This behavior at higher temperatures is not particularly surprising
479 since the densities of both TIP5P and SSD are lower than experimental
480 water densities at higher temperatures. When calculating the
481 diffusion coefficients for SSD at experimental densities
482 (instead of the densities from the NPT simulations), the resulting
483 values fall more in line with experiment at these temperatures.
484
485 \subsection{Structural Changes and Characterization}
486
487 By starting the simulations from the crystalline state, the melting
488 transition and the ice structure can be obtained along with the liquid
489 phase behavior beyond the melting point. The constant pressure heat
490 capacity (C$_\text{p}$) was monitored to locate the melting transition
491 in each of the simulations. In the melting simulations of the 1024
492 particle ice $I_h$ simulations, a large spike in C$_\text{p}$ occurs
493 at 245 K, indicating a first order phase transition for the melting of
494 these ice crystals. When the reaction field is turned off, the melting
495 transition occurs at 235 K. These melting transitions are
496 considerably lower than the experimental value.
497
498 \begin{figure}
499 \begin{center}
500 \epsfxsize=6in
501 \epsfbox{corrDiag.eps}
502 \caption{An illustration of angles involved in the 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 pair correlation functions for
512 512 SSD molecules at 100 K (A \& B) and 300 K (C \& D). Dark areas
513 signify regions of enhanced density while light areas signify
514 depletion relative to the bulk density. White areas have pair
515 correlation values below 0.5 and black 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 pair correlation function,
555 $g_\mathrm{OO}(r)$.\cite{Ichiye96} At low temperatures, the second
556 solvation shell peak appears to have two distinct components that
557 blend together to form one observable peak. At higher temperatures,
558 this split character alters to show the leading 4 \AA\ peak dominated
559 by equatorial anti-parallel dipole orientations. There is also a
560 tightly bunched group of axially arranged dipoles that most likely
561 consist of the smaller fraction of aligned dipole pairs. The trailing
562 component of the split peak at 5 \AA\ is dominated by aligned dipoles
563 that assume hydrogen bond arrangements similar to those seen in the
564 first solvation shell. This evidence indicates that the dipole pair
565 interaction begins to dominate outside of the range of the dipolar
566 repulsion term. The energetically favorable dipole arrangements
567 populate the region immediately outside this repulsion region (around
568 4 \AA), while arrangements that seek to satisfy both the sticky and
569 dipole forces locate themselves just beyond this initial buildup
570 (around 5 \AA).
571
572 From these findings, the split second peak is primarily the product of
573 the dipolar repulsion term of the sticky potential. In fact, the inner
574 peak can be pushed out and merged with the outer split peak just by
575 extending the switching function ($s^\prime(r_{ij})$) from its normal
576 4.0 \AA\ cutoff to values of 4.5 or even 5 \AA. This type of
577 correction is not recommended for improving the liquid structure,
578 since the second solvation shell would still be shifted too far
579 out. In addition, this would have an even more detrimental effect on
580 the system densities, leading to a liquid with a more open structure
581 and a density considerably lower than the already low SSD
582 density. A better correction would be to include the
583 quadrupole-quadrupole interactions for the water particles outside of
584 the first solvation shell, but this would remove the simplicity and
585 speed advantage of SSD.
586
587 \subsection{Adjusted Potentials: SSD/RF and SSD/E}
588
589 The propensity of SSD to adopt lower than expected densities under
590 varying conditions is troubling, especially at higher temperatures. In
591 order to correct this model for use with a reaction field, it is
592 necessary to adjust the force field parameters for the primary
593 intermolecular interactions. In undergoing a reparameterization, it is
594 important not to focus on just one property and neglect the other
595 important properties. In this case, it would be ideal to correct the
596 densities while maintaining the accurate transport behavior.
597
598 The parameters available for tuning include the $\sigma$ and
599 $\epsilon$ Lennard-Jones parameters, the dipole strength ($\mu$), the
600 strength of the sticky potential ($\nu_0$), and the cutoff distances
601 for the sticky attractive and dipole repulsive cubic switching
602 function cutoffs ($r_l$, $r_u$ and $r_l^\prime$, $r_u^\prime$
603 respectively). The results of the reparameterizations are shown in
604 table \ref{params}. We are calling these reparameterizations the Soft
605 Sticky Dipole / Reaction Field (SSD/RF - for use with a reaction
606 field) and Soft Sticky Dipole Extended (SSD/E - an attempt to improve
607 the liquid structure in simulations without a long-range correction).
608
609 \begin{table}
610 \begin{center}
611 \caption{Parameters for the original and adjusted models}
612 \begin{tabular}{ l c c c c }
613 \hline \\[-3mm]
614 \ \ \ Parameters\ \ \ & \ \ \ SSD [Ref. \citen{Ichiye96}] \ \ \
615 & \ SSD1 [Ref. \citen{Ichiye03}]\ \ & \ SSD/E\ \ & \ SSD/RF \\
616 \hline \\[-3mm]
617 \ \ \ $\sigma$ (\AA) & 3.051 & 3.016 & 3.035 & 3.019\\
618 \ \ \ $\epsilon$ (kcal/mol) & 0.152 & 0.152 & 0.152 & 0.152\\
619 \ \ \ $\mu$ (D) & 2.35 & 2.35 & 2.42 & 2.48\\
620 \ \ \ $\nu_0$ (kcal/mol) & 3.7284 & 3.6613 & 3.90 & 3.90\\
621 \ \ \ $\omega^\circ$ & 0.07715 & 0.07715 & 0.07715 & 0.07715\\
622 \ \ \ $r_l$ (\AA) & 2.75 & 2.75 & 2.40 & 2.40\\
623 \ \ \ $r_u$ (\AA) & 3.35 & 3.35 & 3.80 & 3.80\\
624 \ \ \ $r_l^\prime$ (\AA) & 2.75 & 2.75 & 2.75 & 2.75\\
625 \ \ \ $r_u^\prime$ (\AA) & 4.00 & 4.00 & 3.35 & 3.35\\
626 \end{tabular}
627 \label{params}
628 \end{center}
629 \end{table}
630
631 \begin{figure}
632 \begin{center}
633 \epsfxsize=5in
634 \epsfbox{GofRCompare.epsi}
635 \caption{Plots comparing experiment [Ref. \citen{Head-Gordon00_1}] with
636 SSD/E and SSD1 without reaction field (top), as well as
637 SSD/RF and SSD1 with reaction field turned on
638 (bottom). The insets show the respective first peaks in detail. Note
639 how the changes in parameters have lowered and broadened the first
640 peak of SSD/E and SSD/RF.}
641 \label{grcompare}
642 \end{center}
643 \end{figure}
644
645 \begin{figure}
646 \begin{center}
647 \epsfxsize=6in
648 \epsfbox{dualsticky_bw.eps}
649 \caption{Positive and negative isosurfaces of the sticky potential for
650 SSD1 (left) and SSD/E \& SSD/RF (right). Light areas
651 correspond to the tetrahedral attractive component, and darker areas
652 correspond to the dipolar repulsive component.}
653 \label{isosurface}
654 \end{center}
655 \end{figure}
656
657 In the original paper detailing the development of SSD, Liu and Ichiye
658 placed particular emphasis on an accurate description of the first
659 solvation shell. This resulted in a somewhat tall and narrow first
660 peak in $g(r)$ that integrated to give similar coordination numbers to
661 the experimental data obtained by Soper and
662 Phillips.\cite{Ichiye96,Soper86} New experimental x-ray scattering
663 data from the Head-Gordon lab indicates a slightly lower and shifted
664 first peak in the g$_\mathrm{OO}(r)$, so our adjustments to SSD were
665 made after taking into consideration the new experimental
666 findings.\cite{Head-Gordon00_1} Figure \ref{grcompare} shows the
667 relocation of the first peak of the oxygen-oxygen $g(r)$ by comparing
668 the revised SSD model (SSD1), SSD/E, and SSD/RF to the new
669 experimental results. Both modified water models have shorter peaks
670 that match more closely to the experimental peak (as seen in the
671 insets of figure \ref{grcompare}). This structural alteration was
672 accomplished by the combined reduction in the Lennard-Jones $\sigma$
673 variable and adjustment of the sticky potential strength and cutoffs.
674 As can be seen in table \ref{params}, the cutoffs for the tetrahedral
675 attractive and dipolar repulsive terms were nearly swapped with each
676 other. Isosurfaces of the original and modified sticky potentials are
677 shown in figure \ref{isosurface}. In these isosurfaces, it is easy to
678 see how altering the cutoffs changes the repulsive and attractive
679 character of the particles. With a reduced repulsive surface (darker
680 region), the particles can move closer to one another, increasing the
681 density for the overall system. This change in interaction cutoff
682 also results in a more gradual orientational motion by allowing the
683 particles to maintain preferred dipolar arrangements before they begin
684 to feel the pull of the tetrahedral restructuring. As the particles
685 move closer together, the dipolar repulsion term becomes active and
686 excludes unphysical nearest-neighbor arrangements. This compares with
687 how SSD and SSD1 exclude preferred dipole alignments before the
688 particles feel the pull of the ``hydrogen bonds''. Aside from
689 improving the shape of the first peak in the g(\emph{r}), this
690 modification improves the densities considerably by allowing the
691 persistence of full dipolar character below the previous 4.0 \AA\
692 cutoff.
693
694 While adjusting the location and shape of the first peak of $g(r)$
695 improves the densities, these changes alone are insufficient to bring
696 the system densities up to the values observed experimentally. To
697 further increase the densities, the dipole moments were increased in
698 both of our adjusted models. Since SSD is a dipole based model,
699 the structure and transport are very sensitive to changes in the
700 dipole moment. The original SSD simply used the dipole moment
701 calculated from the TIP3P water model, which at 2.35 D is
702 significantly greater than the experimental gas phase value of 1.84
703 D. The larger dipole moment is a more realistic value and improves the
704 dielectric properties of the fluid. Both theoretical and experimental
705 measurements indicate a liquid phase dipole moment ranging from 2.4 D
706 to values as high as 3.11 D, providing a substantial range of
707 reasonable values for a dipole
708 moment.\cite{Sprik91,Kusalik02,Badyal00,Barriol64} Moderately
709 increasing the dipole moments to 2.42 and 2.48 D for SSD/E and
710 SSD/RF, respectively, leads to significant changes in the
711 density and transport of the water models.
712
713 In order to demonstrate the benefits of these reparameterizations, a
714 series of NPT and NVE simulations were performed to probe the density
715 and transport properties of the adapted models and compare the results
716 to the original SSD model. This comparison involved full NPT melting
717 sequences for both SSD/E and SSD/RF, as well as NVE transport
718 calculations at the calculated self-consistent densities. Again, the
719 results are obtained from five separate simulations of 1024 particle
720 systems, and the melting sequences were started from different ice
721 $I_h$ crystals constructed as described previously. Each NPT
722 simulation was equilibrated for 100 ps before a 200 ps data collection
723 run at each temperature step, and the final configuration from the
724 previous temperature simulation was used as a starting point. All NVE
725 simulations had the same thermalization, equilibration, and data
726 collection times as stated previously.
727
728 \begin{figure}
729 \begin{center}
730 \epsfxsize=6in
731 \epsfbox{ssdeDense.epsi}
732 \caption{Comparison of densities calculated with SSD/E to
733 SSD1 without a reaction field, TIP3P [Ref. \citen{Jorgensen98b}],
734 TIP5P [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}] and
735 experiment [Ref. \citen{CRC80}]. The window shows a expansion around
736 300 K with error bars included to clarify this region of
737 interest. Note that both SSD1 and SSD/E show good agreement with
738 experiment when the long-range correction is neglected.}
739 \label{ssdedense}
740 \end{center}
741 \end{figure}
742
743 Fig. \ref{ssdedense} shows the density profile for the SSD/E
744 model in comparison to SSD1 without a reaction field, other
745 common water models, and experimental results. The calculated
746 densities for both SSD/E and SSD1 have increased
747 significantly over the original SSD model (see
748 fig. \ref{dense1}) and are in better agreement with the experimental
749 values. At 298 K, the densities of SSD/E and SSD1 without
750 a long-range correction are 0.996$\pm$0.001 g/cm$^3$ and
751 0.999$\pm$0.001 g/cm$^3$ respectively. These both compare well with
752 the experimental value of 0.997 g/cm$^3$, and they are considerably
753 better than the SSD value of 0.967$\pm$0.003 g/cm$^3$. The
754 changes to the dipole moment and sticky switching functions have
755 improved the structuring of the liquid (as seen in figure
756 \ref{grcompare}, but they have shifted the density maximum to much
757 lower temperatures. This comes about via an increase in the liquid
758 disorder through the weakening of the sticky potential and
759 strengthening of the dipolar character. However, this increasing
760 disorder in the SSD/E model has little effect on the melting
761 transition. By monitoring $C_p$ throughout these simulations, the
762 melting transition for SSD/E was shown to occur at 235 K. The
763 same transition temperature observed with SSD and SSD1.
764
765 \begin{figure}
766 \begin{center}
767 \epsfxsize=6in
768 \epsfbox{ssdrfDense.epsi}
769 \caption{Comparison of densities calculated with SSD/RF to
770 SSD1 with a reaction field, TIP3P [Ref. \citen{Jorgensen98b}],
771 TIP5P [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}], and
772 experiment [Ref. \citen{CRC80}]. The inset shows the necessity of
773 reparameterization when utilizing a reaction field long-ranged
774 correction - SSD/RF provides significantly more accurate
775 densities than SSD1 when performing room temperature
776 simulations.}
777 \label{ssdrfdense}
778 \end{center}
779 \end{figure}
780
781 Including the reaction field long-range correction in the simulations
782 results in a more interesting comparison. A density profile including
783 SSD/RF and SSD1 with an active reaction field is shown in figure
784 \ref{ssdrfdense}. As observed in the simulations without a reaction
785 field, the densities of SSD/RF and SSD1 show a dramatic increase over
786 normal SSD (see figure \ref{dense1}). At 298 K, SSD/RF has a density
787 of 0.997$\pm$0.001 g/cm$^3$, directly in line with experiment and
788 considerably better than the original SSD value of 0.941$\pm$0.001
789 g/cm$^3$ and the SSD1 value of 0.972$\pm$0.002 g/cm$^3$. These results
790 further emphasize the importance of reparameterization in order to
791 model the density properly under different simulation conditions.
792 Again, these changes have only a minor effect on the melting point,
793 which observed at 245 K for SSD/RF, is identical to SSD and only 5 K
794 lower than SSD1 with a reaction field. Additionally, the difference in
795 density maxima is not as extreme, with SSD/RF showing a density
796 maximum at 255 K, fairly close to the density maxima of 260 K and 265
797 K, shown by SSD and SSD1 respectively.
798
799 \begin{figure}
800 \begin{center}
801 \epsfxsize=6in
802 \epsfbox{ssdeDiffuse.epsi}
803 \caption{The diffusion constants calculated from SSD/E and
804 SSD1 (both without a reaction field) along with experimental results
805 [Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations were
806 performed at the average densities observed in the 1 atm NPT
807 simulations for the respective models. SSD/E is slightly more mobile
808 than experiment at all of the temperatures, but it is closer to
809 experiment at biologically relevant temperatures than SSD1 without a
810 long-range correction.}
811 \label{ssdediffuse}
812 \end{center}
813 \end{figure}
814
815 The reparameterization of the SSD water model, both for use with and
816 without an applied long-range correction, brought the densities up to
817 what is expected for simulating liquid water. In addition to improving
818 the densities, it is important that the diffusive behavior of SSD be
819 maintained or improved. Figure \ref{ssdediffuse} compares the
820 temperature dependence of the diffusion constant of SSD/E to SSD1
821 without an active reaction field at the densities calculated from
822 their respective NPT simulations at 1 atm. The diffusion constant for
823 SSD/E is consistently higher than experiment, while SSD1 remains lower
824 than experiment until relatively high temperatures (around 360
825 K). Both models follow the shape of the experimental curve well below
826 300 K but tend to diffuse too rapidly at higher temperatures, as seen
827 in SSD1's crossing above 360 K. This increasing diffusion relative to
828 the experimental values is caused by the rapidly decreasing system
829 density with increasing temperature. Both SSD1 and SSD/E show this
830 deviation in particle mobility, but this trend has different
831 implications on the diffusive behavior of the models. While SSD1
832 shows more experimentally accurate diffusive behavior in the high
833 temperature regimes, SSD/E shows more accurate behavior in the
834 supercooled and biologically relevant temperature ranges. Thus, the
835 changes made to improve the liquid structure may have had an adverse
836 affect on the density maximum, but they improve the transport behavior
837 of SSD/E relative to SSD1 under the most commonly simulated
838 conditions.
839
840 \begin{figure}
841 \begin{center}
842 \epsfxsize=6in
843 \epsfbox{ssdrfDiffuse.epsi}
844 \caption{The diffusion constants calculated from SSD/RF and
845 SSD1 (both with an active reaction field) along with
846 experimental results [Refs. \citen{Gillen72} and \citen{Holz00}]. The
847 NVE calculations were performed at the average densities observed in
848 the 1 atm NPT simulations for both of the models. SSD/RF
849 simulates the diffusion of water throughout this temperature range
850 very well. The rapidly increasing diffusion constants at high
851 temperatures for both models can be attributed to lower calculated
852 densities than those observed in experiment.}
853 \label{ssdrfdiffuse}
854 \end{center}
855 \end{figure}
856
857 In figure \ref{ssdrfdiffuse}, the diffusion constants for SSD/RF are
858 compared to SSD1 with an active reaction field. Note that SSD/RF
859 tracks the experimental results quantitatively, identical within error
860 throughout most of the temperature range shown and exhibiting only a
861 slight increasing trend at higher temperatures. SSD1 tends to diffuse
862 more slowly at low temperatures and deviates to diffuse too rapidly at
863 temperatures greater than 330 K. As stated above, this deviation away
864 from the ideal trend is due to a rapid decrease in density at higher
865 temperatures. SSD/RF does not suffer from this problem as much as SSD1
866 because the calculated densities are closer to the experimental
867 values. These results again emphasize the importance of careful
868 reparameterization when using an altered long-range correction.
869
870 \begin{table}
871 \begin{minipage}{\linewidth}
872 \renewcommand{\thefootnote}{\thempfootnote}
873 \begin{center}
874 \caption{Properties of the single-point water models compared with
875 experimental data at ambient conditions}
876 \begin{tabular}{ l c c c c c }
877 \hline \\[-3mm]
878 \ \ \ \ \ \ & \ \ \ SSD1 \ \ \ & \ SSD/E \ \ \ & \ SSD1 (RF) \ \
879 \ & \ SSD/RF \ \ \ & \ Expt. \\
880 \hline \\[-3mm]
881 \ \ \ $\rho$ (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 \\
882 \ \ \ $C_p$ (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 \\
883 \ \ \ $D$ ($10^{-5}$ cm$^2$/s) & 1.78 $\pm$0.07 & 2.51 $\pm$0.18 &
884 2.00 $\pm$0.17 & 2.32 $\pm$0.06 & 2.299\cite{Mills73} \\
885 \ \ \ Coordination Number ($n_C$) & 3.9 & 4.3 & 3.8 & 4.4 &
886 4.7\footnote{Calculated by integrating $g_{\text{OO}}(r)$ in
887 Ref. \citen{Head-Gordon00_1}} \\
888 \ \ \ H-bonds per particle ($n_H$) & 3.7 & 3.6 & 3.7 & 3.7 &
889 3.5\footnote{Calculated by integrating $g_{\text{OH}}(r)$ in
890 Ref. \citen{Soper86}} \\
891 \ \ \ $\tau_1$ (ps) & 10.9 $\pm$0.6 & 7.3 $\pm$0.4 & 7.5 $\pm$0.7 &
892 7.2 $\pm$0.4 & 5.7\footnote{Calculated for 298 K from data in Ref. \citen{Eisenberg69}} \\
893 \ \ \ $\tau_2$ (ps) & 4.7 $\pm$0.4 & 3.1 $\pm$0.2 & 3.5 $\pm$0.3 & 3.2
894 $\pm$0.2 & 2.3\footnote{Calculated for 298 K from data in
895 Ref. \citen{Krynicki66}}
896 \end{tabular}
897 \label{liquidproperties}
898 \end{center}
899 \end{minipage}
900 \end{table}
901
902 Table \ref{liquidproperties} gives a synopsis of the liquid state
903 properties of the water models compared in this study along with the
904 experimental values for liquid water at ambient conditions. The
905 coordination number ($n_C$) and number of hydrogen bonds per particle
906 ($n_H$) were calculated by integrating the following relations:
907 \begin{equation}
908 n_C = 4\pi\rho_{\text{OO}}\int_{0}^{a}r^2\text{g}_{\text{OO}}(r)dr,
909 \end{equation}
910 \begin{equation}
911 n_H = 4\pi\rho_{\text{OH}}\int_{0}^{b}r^2\text{g}_{\text{OH}}(r)dr,
912 \end{equation}
913 where $\rho$ is the number density of the specified pair interactions,
914 $a$ and $b$ are the radial locations of the minima following the first
915 peak in g$_\text{OO}(r)$ or g$_\text{OH}(r)$ respectively. The number
916 of hydrogen bonds stays relatively constant across all of the models,
917 but the coordination numbers of SSD/E and SSD/RF show an
918 improvement over SSD1. This improvement is primarily due to
919 extension of the first solvation shell in the new parameter sets.
920 Because $n_H$ and $n_C$ are nearly identical in SSD1, it appears
921 that all molecules in the first solvation shell are involved in
922 hydrogen bonds. Since $n_H$ and $n_C$ differ in the newly
923 parameterized models, the orientations in the first solvation shell
924 are a bit more ``fluid''. Therefore SSD1 overstructures the
925 first solvation shell and our reparameterizations have returned this
926 shell to more realistic liquid-like behavior.
927
928 The time constants for the orientational autocorrelation functions
929 are also displayed in Table \ref{liquidproperties}. The dipolar
930 orientational time correlation functions ($C_{l}$) are described
931 by:
932 \begin{equation}
933 C_{l}(t) = \langle P_l[\hat{\mathbf{u}}_j(0)\cdot\hat{\mathbf{u}}_j(t)]\rangle,
934 \end{equation}
935 where $P_l$ are Legendre polynomials of order $l$ and
936 $\hat{\mathbf{u}}_j$ is the unit vector pointing along the molecular
937 dipole.\cite{Rahman71} From these correlation functions, the
938 orientational relaxation time of the dipole vector can be calculated
939 from an exponential fit in the long-time regime ($t >
940 \tau_l$).\cite{Rothschild84} Calculation of these time constants were
941 averaged over five detailed NVE simulations performed at the ambient
942 conditions for each of the respective models. It should be noted that
943 the commonly cited value of 1.9 ps for $\tau_2$ was determined from
944 the NMR data in Ref. \citen{Krynicki66} at a temperature near
945 34$^\circ$C.\cite{Rahman71} Because of the strong temperature
946 dependence of $\tau_2$, it is necessary to recalculate it at 298 K to
947 make proper comparisons. The value shown in Table
948 \ref{liquidproperties} was calculated from the same NMR data in the
949 fashion described in Ref. \citen{Krynicki66}. Similarly, $\tau_1$ was
950 recomputed for 298 K from the data in Ref. \citen{Eisenberg69}.
951 Again, SSD/E and SSD/RF show improved behavior over SSD1, both with
952 and without an active reaction field. Turning on the reaction field
953 leads to much improved time constants for SSD1; however, these results
954 also include a corresponding decrease in system density.
955 Orientational relaxation times published in the original SSD dynamics
956 papers are smaller than the values observed here, and this difference
957 can be attributed to the use of the Ewald sum.\cite{Ichiye99}
958
959 \subsection{Additional Observations}
960
961 \begin{figure}
962 \begin{center}
963 \epsfxsize=6in
964 \epsfbox{icei_bw.eps}
965 \caption{The most stable crystal structure assumed by the SSD family
966 of water models. We refer to this structure as Ice-{\it i} to
967 indicate its origins in computer simulation. This image was taken of
968 the (001) face of the crystal.}
969 \label{weirdice}
970 \end{center}
971 \end{figure}
972
973 While performing a series of melting simulations on an early iteration
974 of SSD/E not discussed in this paper, we observed
975 recrystallization into a novel structure not previously known for
976 water. After melting at 235 K, two of five systems underwent
977 crystallization events near 245 K. The two systems remained
978 crystalline up to 320 and 330 K, respectively. The crystal exhibits
979 an expanded zeolite-like structure that does not correspond to any
980 known form of ice. This appears to be an artifact of the point
981 dipolar models, so to distinguish it from the experimentally observed
982 forms of ice, we have denoted the structure
983 Ice-$\sqrt{\smash[b]{-\text{I}}}$ (Ice-{\it i}). A large enough
984 portion of the sample crystallized that we have been able to obtain a
985 near ideal crystal structure of Ice-{\it i}. Figure \ref{weirdice}
986 shows the repeating crystal structure of a typical crystal at 5
987 K. Each water molecule is hydrogen bonded to four others; however, the
988 hydrogen bonds are bent rather than perfectly straight. This results
989 in a skewed tetrahedral geometry about the central molecule. In
990 figure \ref{isosurface}, it is apparent that these flexed hydrogen
991 bonds are allowed due to the conical shape of the attractive regions,
992 with the greatest attraction along the direct hydrogen bond
993 configuration. Though not ideal, these flexed hydrogen bonds are
994 favorable enough to stabilize an entire crystal generated around them.
995
996 Initial simulations indicated that Ice-{\it i} is the preferred ice
997 structure for at least the SSD/E model. To verify this, a comparison
998 was made between near ideal crystals of ice~$I_h$, ice~$I_c$, and
999 Ice-{\it i} at constant pressure with SSD/E, SSD/RF, and
1000 SSD1. Near-ideal versions of the three types of crystals were cooled
1001 to 1 K, and enthalpies of formation of each were compared using all
1002 three water models. Enthalpies were estimated from the
1003 isobaric-isothermal simulations using $H=U+P_{\text ext}V$ where
1004 $P_{\text ext}$ is the applied pressure. A constant value of -60.158
1005 kcal / mol has been added to place our zero for the enthalpies of
1006 formation for these systems at the traditional state (elemental forms
1007 at standard temperature and pressure). With every model in the SSD
1008 family, Ice-{\it i} had the lowest calculated enthalpy of formation.
1009
1010 \begin{table}
1011 \begin{center}
1012 \caption{Enthalpies of Formation (in kcal / mol) of the three crystal
1013 structures (at 1 K) exhibited by the SSD family of water models}
1014 \begin{tabular}{ l c c c }
1015 \hline \\[-3mm]
1016 \ \ \ Water Model \ \ \ & \ \ \ Ice-$I_h$ \ \ \ & \ Ice-$I_c$\ \ & \
1017 Ice-{\it i} \\
1018 \hline \\[-3mm]
1019 \ \ \ SSD/E & -72.444 & -72.450 & -73.748 \\
1020 \ \ \ SSD/RF & -73.093 & -73.075 & -74.180 \\
1021 \ \ \ SSD1 & -72.654 & -72.569 & -73.575 \\
1022 \ \ \ SSD1 (RF) & -72.662 & -72.569 & -73.292 \\
1023 \end{tabular}
1024 \label{iceenthalpy}
1025 \end{center}
1026 \end{table}
1027
1028 In addition to these energetic comparisons, melting simulations were
1029 performed with ice-{\it i} as the initial configuration using SSD/E,
1030 SSD/RF, and SSD1 both with and without a reaction field. The melting
1031 transitions for both SSD/E and SSD1 without reaction field occurred at
1032 temperature in excess of 375~K. SSD/RF and SSD1 with a reaction field
1033 showed more reasonable melting transitions near 325~K. These melting
1034 point observations clearly show that all of the SSD-derived models
1035 prefer the ice-{\it i} structure.
1036
1037 \section{Conclusions}
1038
1039 The density maximum and temperature dependence of the self-diffusion
1040 constant were studied for the SSD water model, both with and
1041 without the use of reaction field, via a series of NPT and NVE
1042 simulations. The constant pressure simulations showed a density
1043 maximum near 260 K. In most cases, the calculated densities were
1044 significantly lower than the densities obtained from other water
1045 models (and experiment). Analysis of self-diffusion showed SSD
1046 to capture the transport properties of water well in both the liquid
1047 and supercooled liquid regimes.
1048
1049 In order to correct the density behavior, the original SSD model was
1050 reparameterized for use both with and without a reaction field (SSD/RF
1051 and SSD/E), and comparisons were made with SSD1, Ichiye's density
1052 corrected version of SSD. Both models improve the liquid structure,
1053 densities, and diffusive properties under their respective simulation
1054 conditions, indicating the necessity of reparameterization when
1055 changing the method of calculating long-range electrostatic
1056 interactions. In general, however, these simple water models are
1057 excellent choices for representing explicit water in large scale
1058 simulations of biochemical systems.
1059
1060 The existence of a novel low-density ice structure that is preferred
1061 by the SSD family of water models is somewhat troubling, since
1062 liquid simulations on this family of water models at room temperature
1063 are effectively simulations of supercooled or metastable liquids. One
1064 way to destabilize this unphysical ice structure would be to make the
1065 range of angles preferred by the attractive part of the sticky
1066 potential much narrower. This would require extensive
1067 reparameterization to maintain the same level of agreement with the
1068 experiments.
1069
1070 Additionally, our initial calculations show that the Ice-{\it i}
1071 structure may also be a preferred crystal structure for at least one
1072 other popular multi-point water model (TIP3P), and that much of the
1073 simulation work being done using this popular model could also be at
1074 risk for crystallization into this unphysical structure. A future
1075 publication will detail the relative stability of the known ice
1076 structures for a wide range of popular water models.
1077
1078 \section{Acknowledgments}
1079 Support for this project was provided by the National Science
1080 Foundation under grant CHE-0134881. Computation time was provided by
1081 the Notre Dame Bunch-of-Boxes (B.o.B) computer cluster under NSF grant
1082 DMR-0079647.
1083
1084 \newpage
1085
1086 \bibliographystyle{jcp}
1087 \bibliography{nptSSD}
1088
1089 %\pagebreak
1090
1091 \end{document}