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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 chrisfen 1030 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 chrisfen 1030 constant were investigated for the soft sticky dipole (SSD) water
38 gezelter 921 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 chrisfen 1030 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 chrisfen 1030 liquid regimes. We also present our re-parameterized versions of SSD
50 gezelter 921 for use both with the reaction field or without any long-range
51 chrisfen 1030 electrostatic corrections. These are called the SSD/RF and SSD/E
52 gezelter 921 models respectively. These modified models were shown to maintain or
53     improve upon the experimental agreement with the structural and
54 chrisfen 1030 transport properties that can be obtained with either the original SSD
55     or the density corrected version of the original model (SSD1).
56 gezelter 921 Additionally, a novel low-density ice structure is presented
57 chrisfen 1030 which appears to be the most stable ice structure for the entire SSD
58 gezelter 921 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 chrisfen 1030 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 gezelter 921 hard-sphere water model proposed by Bratko, Blum, and
96 chrisfen 1030 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 gezelter 921 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 chrisfen 1030 the proper hydrogen bond orientation in the first solvation shell.
103 gezelter 921
104 chrisfen 1030 The interaction between two SSD water molecules \emph{i} and \emph{j}
105 gezelter 921 is given by the potential
106 chrisfen 743 \begin{equation}
107     u_{ij} = u_{ij}^{LJ} (r_{ij})\ + u_{ij}^{dp}
108 gezelter 921 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)\ +
109 chrisfen 743 u_{ij}^{sp}
110 gezelter 921 ({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j),
111 chrisfen 743 \end{equation}
112 gezelter 921 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 chrisfen 743 \begin{equation}
118 gezelter 921 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 chrisfen 743 \end{equation}
122 gezelter 921 and
123 chrisfen 743 \begin{equation}
124 gezelter 921 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 chrisfen 743 \end{equation}
128 gezelter 921 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 chrisfen 743 \begin{equation}
136     u_{ij}^{sp}
137 gezelter 921 ({\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 chrisfen 1017 \label{stickyfunction}
142 chrisfen 743 \end{equation}
143 gezelter 921 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 chrisfen 743 \begin{equation}
149 gezelter 921 w({\bf r}_{ij},{\bf \Omega}_i,{\bf \Omega}_j)=\sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij},
150 chrisfen 743 \end{equation}
151 gezelter 921 while the $w^\prime$ function counters the normal aligned and
152     anti-aligned structures favored by point dipoles:
153 chrisfen 743 \begin{equation}
154 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,
155 chrisfen 743 \end{equation}
156 gezelter 921 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 chrisfen 1030 can be found in the original SSD
162 gezelter 921 articles.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03}
163 chrisfen 743
164 chrisfen 1030 Since SSD is a single-point {\it dipolar} model, the force
165 gezelter 921 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 chrisfen 1030 SSD decreased computer time by a factor of 6-7 compared to other
169 gezelter 921 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 chrisfen 1030 properties. Indeed, SSD maintains reasonable agreement with the
172     Soper data for the structural features of liquid
173 gezelter 921 water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties
174 chrisfen 1030 exhibited by SSD agree with experiment better than those of more
175 gezelter 921 computationally expensive models (like TIP3P and
176     SPC/E).\cite{Ichiye99} The combination of speed and accurate depiction
177 chrisfen 1030 of solvent properties makes SSD a very attractive model for the
178 gezelter 921 simulation of large scale biochemical simulations.
179 chrisfen 743
180 chrisfen 1030 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 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 1029 \frac{1}{r_{c}^{3}} \sum_{j\in{\mathcal{R}}} {\bf \mu}_{j} s(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 gezelter 1029 moment vector of particle $j$, and $s(r_{ij})$ 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 chrisfen 1022 at the cutoff radius), and as a result we have two reparamaterizations
239 chrisfen 1030 of SSD which could be used either with or without the reaction
240     field turned on.
241 chrisfen 777
242 gezelter 1029 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 chrisfen 1030 simulations of SSD, because there are no explicit hydrogen
251     atoms, and thus no molecular vibrational modes need to be considered.
252 chrisfen 743
253     Integration of the equations of motion was carried out using the
254 chrisfen 1027 symplectic splitting method proposed by Dullweber, Leimkuhler, and
255 chrisfen 1030 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 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 gezelter 1029 The {\sc dlm} method allows for Verlet style integration of both
272 chrisfen 1027 translational and orientational motion of rigid bodies. In this
273 gezelter 921 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 chrisfen 1030 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 gezelter 921 \ref{timestep}.
285 chrisfen 743
286     \begin{figure}
287 chrisfen 862 \begin{center}
288     \epsfxsize=6in
289     \epsfbox{timeStep.epsi}
290 gezelter 1029 \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 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 chrisfen 1030 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 chrisfen 743
311 chrisfen 1030 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 chrisfen 743
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 chrisfen 1030 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 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 chrisfen 1030 Our initial simulations focused on the original SSD water model,
361     and an average density versus temperature plot is shown in figure
362 gezelter 921 \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 chrisfen 1030 \epsfbox{denseSSDnew.eps}
375 gezelter 921 \caption{Density versus temperature for TIP4P [Ref. \citen{Jorgensen98b}],
376 chrisfen 1030 TIP3P [Ref. \citen{Jorgensen98b}], SPC/E [Ref. \citen{Clancy94}], SSD
377     without Reaction Field, SSD, and experiment [Ref. \citen{CRC80}]. The
378 gezelter 921 arrows indicate the change in densities observed when turning off the
379 chrisfen 1030 reaction field. The the lower than expected densities for the SSD
380     model were what prompted the original reparameterization of SSD1
381 gezelter 921 [Ref. \citen{Ichiye03}].}
382 chrisfen 861 \label{dense1}
383 chrisfen 862 \end{center}
384 chrisfen 743 \end{figure}
385    
386 chrisfen 1030 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 chrisfen 743 sources.\cite{Jorgensen98b,Clancy94,CRC80} Of the listed simple water
390 chrisfen 1030 models, SSD has a temperature closest to the experimentally
391     observed density maximum. Of the {\it charge-based} models in
392 gezelter 921 Fig. \ref{dense1}, TIP4P has a density maximum behavior most like that
393 chrisfen 1030 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 gezelter 921 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 chrisfen 1030 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 chrisfen 743
411 chrisfen 862 The key feature to recognize in figure \ref{dense1} is the density
412 chrisfen 1030 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 gezelter 921 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 chrisfen 1030 the curve produced from SSD simulations using reaction field,
427 gezelter 921 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 chrisfen 1027 was what lead Tan {\it et al.} to recently reparameterize
435 chrisfen 1030 SSD.\cite{Ichiye03} Throughout the remainder of the paper our
436     reparamaterizations of SSD will be compared with their newer SSD1
437 gezelter 1029 model.
438 chrisfen 861
439 chrisfen 743 \subsection{Transport Behavior}
440    
441 gezelter 921 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 chrisfen 1022 results.\cite{Gillen72,Holz00,Clancy94,Jorgensen01}
454 gezelter 921
455 chrisfen 743 \begin{figure}
456 chrisfen 862 \begin{center}
457     \epsfxsize=6in
458     \epsfbox{betterDiffuse.epsi}
459 gezelter 921 \caption{Average self-diffusion constant as a function of temperature for
460 chrisfen 1030 SSD, SPC/E [Ref. \citen{Clancy94}], and TIP5P
461 gezelter 1029 [Ref. \citen{Jorgensen01}] compared with experimental data
462     [Refs. \citen{Gillen72} and \citen{Holz00}]. Of the three water models
463 chrisfen 1030 shown, SSD has the least deviation from the experimental values. The
464     rapidly increasing diffusion constants for TIP5P and SSD correspond to
465 gezelter 1029 significant decreases in density at the higher temperatures.}
466 chrisfen 743 \label{diffuse}
467 chrisfen 862 \end{center}
468 chrisfen 743 \end{figure}
469    
470     The observed values for the diffusion constant point out one of the
471 chrisfen 1030 strengths of the SSD model. Of the three models shown, the SSD model
472 gezelter 921 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 chrisfen 1030 correct thermal trend. TIP5P and SSD both start off low at colder
477 gezelter 921 temperatures and tend to diffuse too rapidly at higher temperatures.
478     This behavior at higher temperatures is not particularly surprising
479 chrisfen 1030 since the densities of both TIP5P and SSD are lower than experimental
480 gezelter 921 water densities at higher temperatures. When calculating the
481 chrisfen 1030 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 chrisfen 743
485     \subsection{Structural Changes and Characterization}
486 gezelter 921
487 chrisfen 743 By starting the simulations from the crystalline state, the melting
488 gezelter 921 transition and the ice structure can be obtained along with the liquid
489 chrisfen 862 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 gezelter 921 considerably lower than the experimental value.
497 chrisfen 743
498 chrisfen 862 \begin{figure}
499     \begin{center}
500     \epsfxsize=6in
501     \epsfbox{corrDiag.eps}
502 gezelter 1029 \caption{An illustration of angles involved in the 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 gezelter 1029 \caption{Contour plots of 2D angular pair correlation functions for
512 chrisfen 1030 512 SSD molecules at 100 K (A \& B) and 300 K (C \& D). Dark areas
513 gezelter 1029 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 chrisfen 743 \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 1029 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 chrisfen 743
572     From these findings, the split second peak is primarily the product of
573 chrisfen 861 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 gezelter 921 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 chrisfen 861 correction is not recommended for improving the liquid structure,
578 chrisfen 862 since the second solvation shell would still be shifted too far
579 chrisfen 861 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 chrisfen 1030 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 chrisfen 743
587 chrisfen 1030 \subsection{Adjusted Potentials: SSD/RF and SSD/E}
588 gezelter 921
589 chrisfen 1030 The propensity of SSD to adopt lower than expected densities under
590 chrisfen 743 varying conditions is troubling, especially at higher temperatures. In
591 chrisfen 861 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 gezelter 921 densities while maintaining the accurate transport behavior.
597 chrisfen 743
598 chrisfen 1017 The parameters available for tuning include the $\sigma$ and
599     $\epsilon$ Lennard-Jones parameters, the dipole strength ($\mu$), the
600 gezelter 1029 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 chrisfen 1030 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 gezelter 1029 the liquid structure in simulations without a long-range correction).
608 chrisfen 743
609     \begin{table}
610 chrisfen 862 \begin{center}
611 chrisfen 743 \caption{Parameters for the original and adjusted models}
612 chrisfen 856 \begin{tabular}{ l c c c c }
613 chrisfen 743 \hline \\[-3mm]
614 chrisfen 1030 \ \ \ Parameters\ \ \ & \ \ \ SSD [Ref. \citen{Ichiye96}] \ \ \
615     & \ SSD1 [Ref. \citen{Ichiye03}]\ \ & \ SSD/E\ \ & \ SSD/RF \\
616 chrisfen 743 \hline \\[-3mm]
617 chrisfen 856 \ \ \ $\sigma$ (\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 chrisfen 1017 \ \ \ $\omega^\circ$ & 0.07715 & 0.07715 & 0.07715 & 0.07715\\
622 chrisfen 856 \ \ \ $r_l$ (\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 chrisfen 743 \end{tabular}
627     \label{params}
628 chrisfen 862 \end{center}
629 chrisfen 743 \end{table}
630    
631 chrisfen 862 \begin{figure}
632     \begin{center}
633     \epsfxsize=5in
634     \epsfbox{GofRCompare.epsi}
635 chrisfen 1030 \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 chrisfen 743 \label{grcompare}
642 chrisfen 862 \end{center}
643 chrisfen 743 \end{figure}
644    
645 chrisfen 862 \begin{figure}
646     \begin{center}
647     \epsfxsize=6in
648 chrisfen 1027 \epsfbox{dualsticky_bw.eps}
649 gezelter 1029 \caption{Positive and negative isosurfaces of the sticky potential for
650 chrisfen 1030 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 chrisfen 743 \label{isosurface}
654 chrisfen 862 \end{center}
655 chrisfen 743 \end{figure}
656    
657 chrisfen 1030 In the original paper detailing the development of SSD, Liu and Ichiye
658 gezelter 921 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 chrisfen 862 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 chrisfen 1030 first peak in the g$_\mathrm{OO}(r)$, so our adjustments to SSD were
665 gezelter 1029 made after taking into consideration the new experimental
666 chrisfen 862 findings.\cite{Head-Gordon00_1} Figure \ref{grcompare} shows the
667 gezelter 921 relocation of the first peak of the oxygen-oxygen $g(r)$ by comparing
668 chrisfen 1030 the revised SSD model (SSD1), SSD/E, and SSD/RF to the new
669 chrisfen 862 experimental results. Both modified water models have shorter peaks
670 gezelter 921 that match more closely to the experimental peak (as seen in the
671     insets of figure \ref{grcompare}). This structural alteration was
672 chrisfen 862 accomplished by the combined reduction in the Lennard-Jones $\sigma$
673 gezelter 921 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 chrisfen 1030 density for the overall system. This change in interaction cutoff
682     also results in a more gradual orientational motion by allowing the
683 gezelter 921 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 chrisfen 1030 how SSD and SSD1 exclude preferred dipole alignments before the
688 gezelter 921 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 chrisfen 743
694 gezelter 921 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 chrisfen 1030 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 chrisfen 743
713 chrisfen 861 In order to demonstrate the benefits of these reparameterizations, a
714 chrisfen 743 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 chrisfen 1030 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 chrisfen 861 calculations at the calculated self-consistent densities. Again, the
719 chrisfen 862 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 chrisfen 861 simulation was equilibrated for 100 ps before a 200 ps data collection
723 chrisfen 862 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 gezelter 921 collection times as stated previously.
727 chrisfen 743
728 chrisfen 862 \begin{figure}
729     \begin{center}
730     \epsfxsize=6in
731     \epsfbox{ssdeDense.epsi}
732 chrisfen 1030 \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 gezelter 921 experiment [Ref. \citen{CRC80}]. The window shows a expansion around
736     300 K with error bars included to clarify this region of
737 chrisfen 1030 interest. Note that both SSD1 and SSD/E show good agreement with
738 chrisfen 856 experiment when the long-range correction is neglected.}
739 chrisfen 743 \label{ssdedense}
740 chrisfen 862 \end{center}
741 chrisfen 743 \end{figure}
742    
743 chrisfen 1030 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 chrisfen 862 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 chrisfen 1030 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 chrisfen 743
765 chrisfen 862 \begin{figure}
766     \begin{center}
767     \epsfxsize=6in
768     \epsfbox{ssdrfDense.epsi}
769 chrisfen 1030 \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 gezelter 921 experiment [Ref. \citen{CRC80}]. The inset shows the necessity of
773     reparameterization when utilizing a reaction field long-ranged
774 chrisfen 1030 correction - SSD/RF provides significantly more accurate
775     densities than SSD1 when performing room temperature
776     simulations.}
777 chrisfen 743 \label{ssdrfdense}
778 chrisfen 862 \end{center}
779 chrisfen 743 \end{figure}
780    
781 chrisfen 862 Including the reaction field long-range correction in the simulations
782 gezelter 921 results in a more interesting comparison. A density profile including
783 chrisfen 1030 SSD/RF and SSD1 with an active reaction field is shown in figure
784 chrisfen 862 \ref{ssdrfdense}. As observed in the simulations without a reaction
785 chrisfen 1030 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 chrisfen 862 of 0.997$\pm$0.001 g/cm$^3$, directly in line with experiment and
788 chrisfen 1030 considerably better than the original SSD value of 0.941$\pm$0.001
789     g/cm$^3$ and the SSD1 value of 0.972$\pm$0.002 g/cm$^3$. These results
790 gezelter 921 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 chrisfen 1030 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 gezelter 921 maximum at 255 K, fairly close to the density maxima of 260 K and 265
797 chrisfen 1030 K, shown by SSD and SSD1 respectively.
798 chrisfen 743
799 chrisfen 862 \begin{figure}
800     \begin{center}
801     \epsfxsize=6in
802     \epsfbox{ssdeDiffuse.epsi}
803 chrisfen 1030 \caption{The diffusion constants calculated from SSD/E and
804     SSD1 (both without a reaction field) along with experimental results
805 gezelter 1029 [Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations were
806     performed at the average densities observed in the 1 atm NPT
807 chrisfen 1030 simulations for the respective models. SSD/E is slightly more mobile
808 gezelter 1029 than experiment at all of the temperatures, but it is closer to
809 chrisfen 1030 experiment at biologically relevant temperatures than SSD1 without a
810 gezelter 1029 long-range correction.}
811 chrisfen 861 \label{ssdediffuse}
812 chrisfen 862 \end{center}
813 chrisfen 861 \end{figure}
814    
815 chrisfen 1030 The reparameterization of the SSD water model, both for use with and
816 chrisfen 743 without an applied long-range correction, brought the densities up to
817     what is expected for simulating liquid water. In addition to improving
818 chrisfen 1030 the densities, it is important that the diffusive behavior of SSD be
819 gezelter 1029 maintained or improved. Figure \ref{ssdediffuse} compares the
820 chrisfen 1030 temperature dependence of the diffusion constant of SSD/E to SSD1
821 chrisfen 1027 without an active reaction field at the densities calculated from
822     their respective NPT simulations at 1 atm. The diffusion constant for
823 chrisfen 1030 SSD/E is consistently higher than experiment, while SSD1 remains lower
824 chrisfen 1027 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 chrisfen 1030 in SSD1's crossing above 360 K. This increasing diffusion relative to
828 chrisfen 1027 the experimental values is caused by the rapidly decreasing system
829 chrisfen 1030 density with increasing temperature. Both SSD1 and SSD/E show this
830 chrisfen 1027 deviation in particle mobility, but this trend has different
831 chrisfen 1030 implications on the diffusive behavior of the models. While SSD1
832 chrisfen 1027 shows more experimentally accurate diffusive behavior in the high
833 chrisfen 1030 temperature regimes, SSD/E shows more accurate behavior in the
834 chrisfen 1027 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 chrisfen 1030 of SSD/E relative to SSD1 under the most commonly simulated
838 chrisfen 1027 conditions.
839 chrisfen 743
840 chrisfen 862 \begin{figure}
841     \begin{center}
842     \epsfxsize=6in
843     \epsfbox{ssdrfDiffuse.epsi}
844 chrisfen 1030 \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 chrisfen 856 \label{ssdrfdiffuse}
854 chrisfen 862 \end{center}
855 chrisfen 743 \end{figure}
856    
857 chrisfen 1030 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 gezelter 921 tracks the experimental results quantitatively, identical within error
860 chrisfen 1017 throughout most of the temperature range shown and exhibiting only a
861 chrisfen 1030 slight increasing trend at higher temperatures. SSD1 tends to diffuse
862 chrisfen 1017 more slowly at low temperatures and deviates to diffuse too rapidly at
863 gezelter 921 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 chrisfen 1030 temperatures. SSD/RF does not suffer from this problem as much as SSD1
866 gezelter 921 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 chrisfen 743
870 chrisfen 1017 \begin{table}
871 gezelter 1029 \begin{minipage}{\linewidth}
872     \renewcommand{\thefootnote}{\thempfootnote}
873 chrisfen 1017 \begin{center}
874 gezelter 1029 \caption{Properties of the single-point water models compared with
875     experimental data at ambient conditions}
876 chrisfen 1017 \begin{tabular}{ l c c c c c }
877     \hline \\[-3mm]
878 chrisfen 1030 \ \ \ \ \ \ & \ \ \ SSD1 \ \ \ & \ SSD/E \ \ \ & \ SSD1 (RF) \ \
879     \ & \ SSD/RF \ \ \ & \ Expt. \\
880 chrisfen 1017 \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 gezelter 1029 \ \ \ $D$ ($10^{-5}$ 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$0.2 & 2.3\footnote{Calculated for 298 K from data in
895     Ref. \citen{Krynicki66}}
896 chrisfen 1017 \end{tabular}
897     \label{liquidproperties}
898     \end{center}
899 gezelter 1029 \end{minipage}
900 chrisfen 1017 \end{table}
901    
902     Table \ref{liquidproperties} gives a synopsis of the liquid state
903     properties of the water models compared in this study along with the
904     experimental values for liquid water at ambient conditions. The
905 gezelter 1029 coordination number ($n_C$) and number of hydrogen bonds per particle
906     ($n_H$) were calculated by integrating the following relations:
907 chrisfen 1017 \begin{equation}
908 gezelter 1029 n_C = 4\pi\rho_{\text{OO}}\int_{0}^{a}r^2\text{g}_{\text{OO}}(r)dr,
909 chrisfen 1017 \end{equation}
910 chrisfen 1027 \begin{equation}
911 gezelter 1029 n_H = 4\pi\rho_{\text{OH}}\int_{0}^{b}r^2\text{g}_{\text{OH}}(r)dr,
912 chrisfen 1027 \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 gezelter 1029 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 chrisfen 1030 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 chrisfen 1017
928 gezelter 1029 The time constants for the orientational autocorrelation functions
929 chrisfen 1017 are also displayed in Table \ref{liquidproperties}. The dipolar
930 gezelter 1029 orientational time correlation functions ($C_{l}$) are described
931 chrisfen 1017 by:
932     \begin{equation}
933 gezelter 1029 C_{l}(t) = \langle P_l[\hat{\mathbf{u}}_j(0)\cdot\hat{\mathbf{u}}_j(t)]\rangle,
934 chrisfen 1017 \end{equation}
935 gezelter 1029 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 chrisfen 1022 \ref{liquidproperties} was calculated from the same NMR data in the
949 gezelter 1029 fashion described in Ref. \citen{Krynicki66}. Similarly, $\tau_1$ was
950     recomputed for 298 K from the data in Ref. \citen{Eisenberg69}.
951 chrisfen 1030 Again, SSD/E and SSD/RF show improved behavior over SSD1, both with
952 chrisfen 1027 and without an active reaction field. Turning on the reaction field
953 chrisfen 1030 leads to much improved time constants for SSD1; however, these results
954 gezelter 1029 also include a corresponding decrease in system density.
955 chrisfen 1030 Orientational relaxation times published in the original SSD dynamics
956 gezelter 1029 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 chrisfen 1017
959 chrisfen 743 \subsection{Additional Observations}
960    
961     \begin{figure}
962 chrisfen 862 \begin{center}
963     \epsfxsize=6in
964 chrisfen 1027 \epsfbox{icei_bw.eps}
965 chrisfen 1030 \caption{The most stable crystal structure assumed by the SSD family
966 gezelter 1029 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 chrisfen 743 \label{weirdice}
970 chrisfen 862 \end{center}
971 chrisfen 743 \end{figure}
972    
973 gezelter 921 While performing a series of melting simulations on an early iteration
974 chrisfen 1030 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 gezelter 1029 Ice-$\sqrt{\smash[b]{-\text{I}}}$ (Ice-{\it i}). A large enough
984 gezelter 921 portion of the sample crystallized that we have been able to obtain a
985 gezelter 1029 near ideal crystal structure of Ice-{\it i}. Figure \ref{weirdice}
986 gezelter 921 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 chrisfen 863 configuration. Though not ideal, these flexed hydrogen bonds are
994 gezelter 921 favorable enough to stabilize an entire crystal generated around them.
995 chrisfen 743
996 gezelter 1029 Initial simulations indicated that Ice-{\it i} is the preferred ice
997 chrisfen 1030 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 chrisfen 743
1010 gezelter 921 \begin{table}
1011     \begin{center}
1012 gezelter 1029 \caption{Enthalpies of Formation (in kcal / mol) of the three crystal
1013 chrisfen 1030 structures (at 1 K) exhibited by the SSD family of water models}
1014 gezelter 921 \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 chrisfen 1030 \ \ \ 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 gezelter 921 \end{tabular}
1024     \label{iceenthalpy}
1025     \end{center}
1026     \end{table}
1027 chrisfen 743
1028 gezelter 921 In addition to these energetic comparisons, melting simulations were
1029 chrisfen 1030 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 gezelter 921 showed more reasonable melting transitions near 325~K. These melting
1034 chrisfen 1030 point observations clearly show that all of the SSD-derived models
1035 gezelter 921 prefer the ice-{\it i} structure.
1036 chrisfen 743
1037     \section{Conclusions}
1038    
1039 gezelter 921 The density maximum and temperature dependence of the self-diffusion
1040 chrisfen 1030 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 gezelter 921 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 chrisfen 1030 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 gezelter 921
1049 chrisfen 1030 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 gezelter 921 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 chrisfen 1030 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 chrisfen 1027 way to destabilize this unphysical ice structure would be to make the
1065 gezelter 921 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 gezelter 1029 Additionally, our initial calculations show that the Ice-{\it i}
1071 gezelter 921 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 chrisfen 743 \section{Acknowledgments}
1079 chrisfen 777 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 gezelter 921 DMR-0079647.
1083 chrisfen 743
1084 chrisfen 862 \newpage
1085    
1086 chrisfen 743 \bibliographystyle{jcp}
1087     \bibliography{nptSSD}
1088    
1089     %\pagebreak
1090    
1091     \end{document}