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1 chrisfen 861 %\documentclass[prb,aps,times,twocolumn,tabularx]{revtex4}
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21 chrisfen 743
22     \begin{document}
23    
24 gezelter 921 \title{On the structural and transport properties of the soft sticky
25     dipole (SSD) and related single point water models}
26 chrisfen 743
27 chrisfen 862 \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 chrisfen 743 Notre Dame, Indiana 46556}
30    
31     \date{\today}
32    
33 chrisfen 862 \maketitle
34    
35 chrisfen 743 \begin{abstract}
36 gezelter 921 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 chrisfen 861 experimental water very well in both the normal and super-cooled
49 gezelter 921 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 chrisfen 743 \end{abstract}
60    
61 chrisfen 862 \newpage
62 chrisfen 743
63     %\narrowtext
64    
65    
66     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
67     % BODY OF TEXT
68     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
69    
70     \section{Introduction}
71    
72 chrisfen 862 One of the most important tasks in the simulation of biochemical
73 gezelter 921 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 chrisfen 743
81 gezelter 921 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 chrisfen 743 \begin{equation}
108     u_{ij} = u_{ij}^{LJ} (r_{ij})\ + u_{ij}^{dp}
109 gezelter 921 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)\ +
110 chrisfen 743 u_{ij}^{sp}
111 gezelter 921 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j),
112 chrisfen 743 \end{equation}
113 gezelter 921 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 chrisfen 743 \begin{equation}
119 gezelter 921 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 chrisfen 743 \end{equation}
123 gezelter 921 and
124 chrisfen 743 \begin{equation}
125 gezelter 921 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 chrisfen 743 \end{equation}
129 gezelter 921 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 chrisfen 743 \begin{equation}
137     u_{ij}^{sp}
138 gezelter 921 ({\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 chrisfen 1017 \label{stickyfunction}
143 chrisfen 743 \end{equation}
144 gezelter 921 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 chrisfen 743 \begin{equation}
150 gezelter 921 w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)=\sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij},
151 chrisfen 743 \end{equation}
152 gezelter 921 while the $w^\prime$ function counters the normal aligned and
153     anti-aligned structures favored by point dipoles:
154 chrisfen 743 \begin{equation}
155 chrisfen 1017 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 chrisfen 743 \end{equation}
157 gezelter 921 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 chrisfen 743
165 gezelter 921 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 chrisfen 743
181 gezelter 921 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 chrisfen 757
208 chrisfen 743 \section{Methods}
209    
210 gezelter 921 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 chrisfen 1019 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 chrisfen 743 \begin{equation}
217     \mathcal{E}_{i} = \frac{2(\varepsilon_{s} - 1)}{2\varepsilon_{s} + 1}
218 gezelter 921 \frac{1}{r_{c}^{3}} \sum_{j\in{\mathcal{R}}} {\bf \mu}_{j} f(r_{ij})\ ,
219 chrisfen 743 \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 gezelter 921 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 chrisfen 743 function.\cite{AllenTildesley} The reaction field contribution to the
226 gezelter 921 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 chrisfen 777
242 gezelter 921 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 chrisfen 743
253     Integration of the equations of motion was carried out using the
254 gezelter 921 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 chrisfen 743
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 gezelter 921 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 chrisfen 743
271     The symplectic splitting method allows for Verlet style integration of
272 gezelter 921 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 chrisfen 743
286     \begin{figure}
287 chrisfen 862 \begin{center}
288     \epsfxsize=6in
289     \epsfbox{timeStep.epsi}
290 gezelter 921 \caption{Energy conservation using both quaternion based integration and
291 chrisfen 743 the symplectic step method proposed by Dullweber \emph{et al.} with
292 gezelter 921 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 chrisfen 743 \label{timestep}
295 chrisfen 862 \end{center}
296 chrisfen 743 \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 gezelter 921 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 chrisfen 743
311 chrisfen 862 Energy drift in the symplectic step simulations was unnoticeable for
312 gezelter 921 time steps up to 3 fs. A slight energy drift on the
313 chrisfen 743 order of 0.012 kcal/mol per nanosecond was observed at a time step of
314 gezelter 921 4 fs, and as expected, this drift increases dramatically
315     with increasing time step. To insure accuracy in our microcanonical
316 chrisfen 743 simulations, time steps were set at 2 fs and kept at this value for
317     constant pressure simulations as well.
318    
319 gezelter 921 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 chrisfen 743 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 chrisfen 862 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 chrisfen 743 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 chrisfen 862 rules.\cite{Bernal33,Rahman72} This method was also utilized in the
335 chrisfen 743 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 gezelter 921 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 chrisfen 743
358     \subsection{Density Behavior}
359    
360 gezelter 921 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 chrisfen 743 \begin{figure}
372 chrisfen 862 \begin{center}
373     \epsfxsize=6in
374     \epsfbox{denseSSD.eps}
375 gezelter 921 \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 chrisfen 861 \label{dense1}
383 chrisfen 862 \end{center}
384 chrisfen 743 \end{figure}
385    
386 gezelter 921 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 chrisfen 743 sources.\cite{Jorgensen98b,Clancy94,CRC80} Of the listed simple water
390 gezelter 921 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 chrisfen 743
397 gezelter 921 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 chrisfen 743
411 chrisfen 862 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 gezelter 921 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 chrisfen 861 reaction field, the density around 300 K is still significantly lower
433     than experiment and comparable water models. This anomalous behavior
434 gezelter 921 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 chrisfen 861
438 chrisfen 743 \subsection{Transport Behavior}
439    
440 gezelter 921 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 chrisfen 743 \begin{figure}
455 chrisfen 862 \begin{center}
456     \epsfxsize=6in
457     \epsfbox{betterDiffuse.epsi}
458 gezelter 921 \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 chrisfen 743 \label{diffuse}
466 chrisfen 862 \end{center}
467 chrisfen 743 \end{figure}
468    
469     The observed values for the diffusion constant point out one of the
470 gezelter 921 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 chrisfen 743
484     \subsection{Structural Changes and Characterization}
485 gezelter 921
486 chrisfen 743 By starting the simulations from the crystalline state, the melting
487 gezelter 921 transition and the ice structure can be obtained along with the liquid
488 chrisfen 862 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 gezelter 921 considerably lower than the experimental value.
496 chrisfen 743
497 chrisfen 862 \begin{figure}
498     \begin{center}
499     \epsfxsize=6in
500     \epsfbox{corrDiag.eps}
501     \caption{Two dimensional illustration of angles involved in the
502 gezelter 921 correlations observed in Fig. \ref{contour}.}
503 chrisfen 862 \label{corrAngle}
504     \end{center}
505     \end{figure}
506    
507     \begin{figure}
508     \begin{center}
509     \epsfxsize=6in
510     \epsfbox{fullContours.eps}
511 chrisfen 743 \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 gezelter 921 depressions. White areas have $g(r)$ values below 0.5 and black
515 chrisfen 743 areas have values above 1.5.}
516     \label{contour}
517 chrisfen 862 \end{center}
518 chrisfen 743 \end{figure}
519    
520 gezelter 921 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 chrisfen 861
524 chrisfen 862 \begin{equation}
525 gezelter 921 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 chrisfen 862 \end{equation}
527     \begin{equation}
528     g_{\text{AB}}(r,\cos\omega) =
529 gezelter 921 \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 chrisfen 862 \end{equation}
531 chrisfen 861 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 gezelter 921 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 chrisfen 861 bonding arrangements as dictated by the tetrahedral sticky potential -
539 gezelter 921 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 chrisfen 743 which decays at distances around the fourth solvation shell, near the
543     imposed cutoff for the Lennard-Jones and dipole-dipole interactions.
544 chrisfen 861 In the higher temperature simulation shown in frames C and D, these
545 gezelter 921 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 chrisfen 743
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 gezelter 921 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 chrisfen 862 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 gezelter 921 dipolar repulsion term. The energetically favorable dipole
566 chrisfen 862 arrangements populate the region immediately outside this repulsion
567 gezelter 921 region (around 4 \AA), while arrangements that seek to satisfy both
568     the sticky and dipole forces locate themselves just beyond this
569 chrisfen 862 initial buildup (around 5 \AA).
570 chrisfen 743
571     From these findings, the split second peak is primarily the product of
572 chrisfen 861 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 gezelter 921 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 chrisfen 861 correction is not recommended for improving the liquid structure,
577 chrisfen 862 since the second solvation shell would still be shifted too far
578 chrisfen 861 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 gezelter 921 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 chrisfen 743
586 chrisfen 861 \subsection{Adjusted Potentials: SSD/RF and SSD/E}
587 gezelter 921
588 chrisfen 743 The propensity of SSD to adopt lower than expected densities under
589     varying conditions is troubling, especially at higher temperatures. In
590 chrisfen 861 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 gezelter 921 densities while maintaining the accurate transport behavior.
596 chrisfen 743
597 chrisfen 1017 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 gezelter 921 (SSD/RF - for use with a reaction field) and Soft Sticky Dipole
605 chrisfen 1017 Extended (SSD/E - an attempt to improve the liquid structure in
606 chrisfen 862 simulations without a long-range correction).
607 chrisfen 743
608     \begin{table}
609 chrisfen 862 \begin{center}
610 chrisfen 743 \caption{Parameters for the original and adjusted models}
611 chrisfen 856 \begin{tabular}{ l c c c c }
612 chrisfen 743 \hline \\[-3mm]
613 gezelter 921 \ \ \ Parameters\ \ \ & \ \ \ SSD [Ref. \citen{Ichiye96}] \ \ \
614     & \ SSD1 [Ref. \citen{Ichiye03}]\ \ & \ SSD/E\ \ & \ SSD/RF \\
615 chrisfen 743 \hline \\[-3mm]
616 chrisfen 856 \ \ \ $\sigma$ (\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 chrisfen 1017 \ \ \ $\omega^\circ$ & 0.07715 & 0.07715 & 0.07715 & 0.07715\\
621 chrisfen 856 \ \ \ $r_l$ (\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 chrisfen 743 \end{tabular}
626     \label{params}
627 chrisfen 862 \end{center}
628 chrisfen 743 \end{table}
629    
630 chrisfen 862 \begin{figure}
631     \begin{center}
632     \epsfxsize=5in
633     \epsfbox{GofRCompare.epsi}
634 gezelter 921 \caption{Plots comparing experiment [Ref. \citen{Head-Gordon00_1}] with SSD/E
635 chrisfen 856 and SSD1 without reaction field (top), as well as SSD/RF and SSD1 with
636 chrisfen 743 reaction field turned on (bottom). The insets show the respective
637 chrisfen 862 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 chrisfen 743 \label{grcompare}
640 chrisfen 862 \end{center}
641 chrisfen 743 \end{figure}
642    
643 chrisfen 862 \begin{figure}
644     \begin{center}
645     \epsfxsize=6in
646     \epsfbox{dualsticky.ps}
647 chrisfen 856 \caption{Isosurfaces of the sticky potential for SSD1 (left) and SSD/E \&
648 chrisfen 743 SSD/RF (right). Light areas correspond to the tetrahedral attractive
649 chrisfen 862 component, and darker areas correspond to the dipolar repulsive
650     component.}
651 chrisfen 743 \label{isosurface}
652 chrisfen 862 \end{center}
653 chrisfen 743 \end{figure}
654    
655 gezelter 921 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 chrisfen 862 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 gezelter 921 first peak in the g$_\mathrm{OO}(r)$, so our adjustments to SSD were
663     made while taking into consideration the new experimental
664 chrisfen 862 findings.\cite{Head-Gordon00_1} Figure \ref{grcompare} shows the
665 gezelter 921 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 chrisfen 862 experimental results. Both modified water models have shorter peaks
668 gezelter 921 that match more closely to the experimental peak (as seen in the
669     insets of figure \ref{grcompare}). This structural alteration was
670 chrisfen 862 accomplished by the combined reduction in the Lennard-Jones $\sigma$
671 gezelter 921 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 chrisfen 743
692 gezelter 921 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 chrisfen 862 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 chrisfen 743
710 chrisfen 861 In order to demonstrate the benefits of these reparameterizations, a
711 chrisfen 743 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 chrisfen 861 calculations at the calculated self-consistent densities. Again, the
716 chrisfen 862 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 chrisfen 861 simulation was equilibrated for 100 ps before a 200 ps data collection
720 chrisfen 862 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 gezelter 921 collection times as stated previously.
724 chrisfen 743
725 chrisfen 862 \begin{figure}
726     \begin{center}
727     \epsfxsize=6in
728     \epsfbox{ssdeDense.epsi}
729 chrisfen 861 \caption{Comparison of densities calculated with SSD/E to SSD1 without a
730 gezelter 921 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 chrisfen 856 experiment when the long-range correction is neglected.}
736 chrisfen 743 \label{ssdedense}
737 chrisfen 862 \end{center}
738 chrisfen 743 \end{figure}
739    
740 gezelter 921 Fig. \ref{ssdedense} shows the density profile for the SSD/E model
741 chrisfen 862 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 gezelter 921 model (see fig. \ref{dense1}) and are in better agreement with the
745 chrisfen 862 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 gezelter 921 little effect on the melting transition. By monitoring $C_p$
757 chrisfen 862 throughout these simulations, the melting transition for SSD/E was
758 gezelter 921 shown to occur at 235 K. The same transition temperature observed
759     with SSD and SSD1.
760 chrisfen 743
761 chrisfen 862 \begin{figure}
762     \begin{center}
763     \epsfxsize=6in
764     \epsfbox{ssdrfDense.epsi}
765 chrisfen 861 \caption{Comparison of densities calculated with SSD/RF to SSD1 with a
766 gezelter 921 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 chrisfen 743 \label{ssdrfdense}
773 chrisfen 862 \end{center}
774 chrisfen 743 \end{figure}
775    
776 chrisfen 862 Including the reaction field long-range correction in the simulations
777 gezelter 921 results in a more interesting comparison. A density profile including
778 chrisfen 862 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$, directly in line with experiment and
783 gezelter 921 considerably better than the original SSD value of 0.941$\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 chrisfen 743
794 chrisfen 862 \begin{figure}
795     \begin{center}
796     \epsfxsize=6in
797     \epsfbox{ssdeDiffuse.epsi}
798 chrisfen 1017 \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 chrisfen 861 \label{ssdediffuse}
807 chrisfen 862 \end{center}
808 chrisfen 861 \end{figure}
809    
810 chrisfen 743 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 gezelter 921 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 chrisfen 1017 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 chrisfen 743
834 chrisfen 862 \begin{figure}
835     \begin{center}
836     \epsfxsize=6in
837     \epsfbox{ssdrfDiffuse.epsi}
838 chrisfen 1017 \caption{The diffusion constants calculated from SSD/RF and SSD1,
839 gezelter 921 both with an active reaction field, along with experimental results
840 chrisfen 1017 [Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations
841 gezelter 921 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 chrisfen 1017 temperatures for both models is attributed to lower calculated
846     densities than those observed in experiment.}
847 chrisfen 856 \label{ssdrfdiffuse}
848 chrisfen 862 \end{center}
849 chrisfen 743 \end{figure}
850    
851     In figure \ref{ssdrfdiffuse}, the diffusion constants for SSD/RF are
852 chrisfen 862 compared to SSD1 with an active reaction field. Note that SSD/RF
853 gezelter 921 tracks the experimental results quantitatively, identical within error
854 chrisfen 1017 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 gezelter 921 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 chrisfen 743
864 chrisfen 1017 \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 chrisfen 1019 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 chrisfen 1017
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 chrisfen 1019 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 chrisfen 1017
929 chrisfen 743 \subsection{Additional Observations}
930    
931     \begin{figure}
932 chrisfen 862 \begin{center}
933     \epsfxsize=6in
934     \epsfbox{povIce.ps}
935     \caption{A water lattice built from the crystal structure assumed by
936 gezelter 921 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 chrisfen 743 \label{weirdice}
941 chrisfen 862 \end{center}
942 chrisfen 743 \end{figure}
943    
944 gezelter 921 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 chrisfen 863 configuration. Though not ideal, these flexed hydrogen bonds are
964 gezelter 921 favorable enough to stabilize an entire crystal generated around them.
965 chrisfen 743
966 gezelter 921 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 chrisfen 743
977 gezelter 921 \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 chrisfen 743
995 gezelter 921 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 chrisfen 743
1004     \section{Conclusions}
1005    
1006 gezelter 921 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 chrisfen 743 \section{Acknowledgments}
1046 chrisfen 777 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 gezelter 921 DMR-0079647.
1050 chrisfen 743
1051 chrisfen 862 \newpage
1052    
1053 chrisfen 743 \bibliographystyle{jcp}
1054     \bibliography{nptSSD}
1055    
1056     %\pagebreak
1057    
1058     \end{document}