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\begin{document} |
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\title{On the structural and transport properties of the soft sticky |
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dipole ({\sc ssd}) and related single point water models} |
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dipole (SSD) and related single point water models} |
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|
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\author{Christopher J. Fennell and J. Daniel Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\ |
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Department of Chemistry and Biochemistry\\ University of Notre Dame\\ |
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\begin{abstract} |
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The density maximum and temperature dependence of the self-diffusion |
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constant were investigated for the soft sticky dipole ({\sc ssd}) water |
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constant were investigated for the soft sticky dipole (SSD) water |
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model and two related re-parameterizations of this single-point model. |
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A combination of microcanonical and isobaric-isothermal molecular |
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dynamics simulations were used to calculate these properties, both |
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260 K. In most cases, the use of the reaction field resulted in |
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calculated densities which were were significantly lower than |
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experimental densities. Analysis of self-diffusion constants shows |
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that the original {\sc ssd} model captures the transport properties of |
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that the original SSD model captures the transport properties of |
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experimental water very well in both the normal and super-cooled |
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liquid regimes. We also present our re-parameterized versions of {\sc ssd} |
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liquid regimes. We also present our re-parameterized versions of SSD |
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for use both with the reaction field or without any long-range |
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electrostatic corrections. These are called the {\sc ssd/rf} and {\sc ssd/e} |
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electrostatic corrections. These are called the SSD/RF and SSD/E |
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models respectively. These modified models were shown to maintain or |
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improve upon the experimental agreement with the structural and |
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transport properties that can be obtained with either the original {\sc ssd} |
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or the density corrected version of the original model ({\sc ssd1}). |
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transport properties that can be obtained with either the original SSD |
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or the density corrected version of the original model (SSD1). |
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Additionally, a novel low-density ice structure is presented |
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which appears to be the most stable ice structure for the entire {\sc ssd} |
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which appears to be the most stable ice structure for the entire SSD |
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family. |
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\end{abstract} |
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One recently developed model that largely succeeds in retaining the |
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accuracy of bulk properties while greatly reducing the computational |
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cost is the Soft Sticky Dipole ({\sc ssd}) water |
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model.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03} The {\sc ssd} model was |
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developed by Ichiye \emph{et al.} as a modified form of the |
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cost is the Soft Sticky Dipole (SSD) water |
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model.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03} The SSD model |
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was developed by Ichiye \emph{et al.} as a modified form of the |
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hard-sphere water model proposed by Bratko, Blum, and |
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Luzar.\cite{Bratko85,Bratko95} {\sc ssd} is a {\it single point} model which |
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has an interaction site that is both a point dipole along with a |
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Luzar.\cite{Bratko85,Bratko95} SSD is a {\it single point} model |
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which has an interaction site that is both a point dipole along with a |
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Lennard-Jones core. However, since the normal aligned and |
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anti-aligned geometries favored by point dipoles are poor mimics of |
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local structure in liquid water, a short ranged ``sticky'' potential |
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is also added. The sticky potential directs the molecules to assume |
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the proper hydrogen bond orientation in the first solvation |
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shell. |
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the proper hydrogen bond orientation in the first solvation shell. |
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|
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The interaction between two {\sc ssd} water molecules \emph{i} and \emph{j} |
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The interaction between two SSD water molecules \emph{i} and \emph{j} |
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is given by the potential |
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\begin{equation} |
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u_{ij} = u_{ij}^{LJ} (r_{ij})\ + u_{ij}^{dp} |
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enhances the tetrahedral geometry for hydrogen bonded structures), |
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while $w^\prime$ is a purely empirical function. A more detailed |
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description of the functional parts and variables in this potential |
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can be found in the original {\sc ssd} |
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can be found in the original SSD |
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articles.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03} |
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|
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Since {\sc ssd} is a single-point {\it dipolar} model, the force |
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Since SSD is a single-point {\it dipolar} model, the force |
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calculations are simplified significantly relative to the standard |
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{\it charged} multi-point models. In the original Monte Carlo |
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simulations using this model, Ichiye {\it et al.} reported that using |
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{\sc ssd} decreased computer time by a factor of 6-7 compared to other |
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SSD decreased computer time by a factor of 6-7 compared to other |
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models.\cite{Ichiye96} What is most impressive is that this savings |
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did not come at the expense of accurate depiction of the liquid state |
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properties. Indeed, {\sc ssd} maintains reasonable agreement with the Soper |
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data for the structural features of liquid |
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properties. Indeed, SSD maintains reasonable agreement with the |
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Soper data for the structural features of liquid |
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water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties |
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exhibited by {\sc ssd} agree with experiment better than those of more |
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exhibited by SSD agree with experiment better than those of more |
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computationally expensive models (like TIP3P and |
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SPC/E).\cite{Ichiye99} The combination of speed and accurate depiction |
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of solvent properties makes {\sc ssd} a very attractive model for the |
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of solvent properties makes SSD a very attractive model for the |
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simulation of large scale biochemical simulations. |
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One feature of the {\sc ssd} model is that it was parameterized for use with |
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the Ewald sum to handle long-range interactions. This would normally |
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be the best way of handling long-range interactions in systems that |
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contain other point charges. However, our group has recently become |
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interested in systems with point dipoles as mimics for neutral, but |
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polarized regions on molecules (e.g. the zwitterionic head group |
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regions of phospholipids). If the system of interest does not contain |
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point charges, the Ewald sum and even particle-mesh Ewald become |
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computational bottlenecks. Their respective ideal $N^\frac{3}{2}$ and |
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$N\log N$ calculation scaling orders for $N$ particles can become |
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prohibitive when $N$ becomes large.\cite{Darden99} In applying this |
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water model in these types of systems, it would be useful to know its |
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properties and behavior under the more computationally efficient |
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reaction field (RF) technique, or even with a simple cutoff. This |
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study addresses these issues by looking at the structural and |
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transport behavior of {\sc ssd} over a variety of temperatures with the |
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purpose of utilizing the RF correction technique. We then suggest |
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modifications to the parameters that result in more realistic bulk |
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phase behavior. It should be noted that in a recent publication, some |
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of the original investigators of the {\sc ssd} water model have suggested |
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adjustments to the {\sc ssd} water model to address abnormal density |
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behavior (also observed here), calling the corrected model |
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{\sc ssd1}.\cite{Ichiye03} In what follows, we compare our |
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reparamaterization of {\sc ssd} with both the original {\sc ssd} and {\sc ssd1} models |
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with the goal of improving the bulk phase behavior of an {\sc ssd}-derived |
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model in simulations utilizing the Reaction Field. |
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One feature of the SSD model is that it was parameterized for |
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use with the Ewald sum to handle long-range interactions. This would |
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normally be the best way of handling long-range interactions in |
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systems that contain other point charges. However, our group has |
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recently become interested in systems with point dipoles as mimics for |
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neutral, but polarized regions on molecules (e.g. the zwitterionic |
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head group regions of phospholipids). If the system of interest does |
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not contain point charges, the Ewald sum and even particle-mesh Ewald |
| 188 |
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become computational bottlenecks. Their respective ideal |
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$N^\frac{3}{2}$ and $N\log N$ calculation scaling orders for $N$ |
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particles can become prohibitive when $N$ becomes |
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large.\cite{Darden99} In applying this water model in these types of |
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systems, it would be useful to know its properties and behavior under |
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the more computationally efficient reaction field (RF) technique, or |
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even with a simple cutoff. This study addresses these issues by |
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looking at the structural and transport behavior of SSD over a |
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variety of temperatures with the purpose of utilizing the RF |
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correction technique. We then suggest modifications to the parameters |
| 198 |
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that result in more realistic bulk phase behavior. It should be noted |
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that in a recent publication, some of the original investigators of |
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the SSD water model have suggested adjustments to the SSD |
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water model to address abnormal density behavior (also observed here), |
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calling the corrected model SSD1.\cite{Ichiye03} In what |
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follows, we compare our reparamaterization of SSD with both the |
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original SSD and SSD1 models with the goal of improving |
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the bulk phase behavior of an SSD-derived model in simulations |
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utilizing the Reaction Field. |
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|
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\section{Methods} |
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We have also performed a companion set of simulations {\it without} a |
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surrounding dielectric (i.e. using a simple cubic switching function |
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at the cutoff radius), and as a result we have two reparamaterizations |
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of {\sc ssd} which could be used either with or without the reaction field |
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turned on. |
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of SSD which could be used either with or without the reaction |
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field turned on. |
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Simulations to obtain the preferred densities of the models were |
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performed in the isobaric-isothermal (NPT) ensemble, while all |
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implemented using an integral thermostat and barostat as outlined by |
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Hoover.\cite{Hoover85,Hoover86} All molecules were treated as |
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non-linear rigid bodies. Vibrational constraints are not necessary in |
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simulations of {\sc ssd}, because there are no explicit hydrogen atoms, and |
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thus no molecular vibrational modes need to be considered. |
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simulations of SSD, because there are no explicit hydrogen |
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atoms, and thus no molecular vibrational modes need to be considered. |
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|
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Integration of the equations of motion was carried out using the |
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symplectic splitting method proposed by Dullweber, Leimkuhler, and |
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McLachlan ({\sc dlm}).\cite{Dullweber1997} Our reason for selecting this |
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integrator centers on poor energy conservation of rigid body dynamics |
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using traditional quaternion integration.\cite{Evans77,Evans77b} In |
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typical microcanonical ensemble simulations, the energy drift when |
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using quaternions was substantially greater than when using the {\sc dlm} |
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method (fig. \ref{timestep}). This steady drift in the total energy |
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has also been observed by Kol {\it et al.}\cite{Laird97} |
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McLachlan ({\sc dlm}).\cite{Dullweber1997} Our reason for selecting |
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this integrator centers on poor energy conservation of rigid body |
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dynamics using traditional quaternion |
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integration.\cite{Evans77,Evans77b} In typical microcanonical ensemble |
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simulations, the energy drift when using quaternions was substantially |
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greater than when using the {\sc dlm} method (fig. \ref{timestep}). |
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This steady drift in the total energy has also been observed by Kol |
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{\it et al.}\cite{Laird97} |
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|
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The key difference in the integration method proposed by Dullweber |
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\emph{et al.} is that the entire rotation matrix is propagated from |
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of matrix evaluations to update the rotation |
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matrix.\cite{Dullweber1997} These matrix rotations are more costly |
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than the simpler arithmetic quaternion propagation. With the same time |
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step, a 1000 {\sc ssd} particle simulation shows an average 7\% increase in |
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computation time using the {\sc dlm} method in place of quaternions. The |
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additional expense per step is justified when one considers the |
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ability to use time steps that are nearly twice as large under {\sc dlm} |
| 281 |
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than would be usable under quaternion dynamics. The energy |
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conservation of the two methods using a number of different time steps |
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is illustrated in figure |
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step, a 1000 SSD particle simulation shows an average 7\% |
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increase in computation time using the {\sc dlm} method in place of |
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quaternions. The additional expense per step is justified when one |
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considers the ability to use time steps that are nearly twice as large |
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under {\sc dlm} than would be usable under quaternion dynamics. The |
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energy conservation of the two methods using a number of different |
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time steps is illustrated in figure |
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\ref{timestep}. |
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|
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\begin{figure} |
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\end{figure} |
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|
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In figure \ref{timestep}, the resulting energy drift at various time |
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steps for both the {\sc dlm} and quaternion integration schemes is compared. |
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All of the 1000 {\sc ssd} particle simulations started with the same |
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configuration, and the only difference was the method used to handle |
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orientational motion. At time steps of 0.1 and 0.5 fs, both methods |
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for propagating the orientational degrees of freedom conserve energy |
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fairly well, with the quaternion method showing a slight energy drift |
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over time in the 0.5 fs time step simulation. At time steps of 1 and 2 |
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fs, the energy conservation benefits of the {\sc dlm} method are clearly |
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demonstrated. Thus, while maintaining the same degree of energy |
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conservation, one can take considerably longer time steps, leading to |
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an overall reduction in computation time. |
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steps for both the {\sc dlm} and quaternion integration schemes is |
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compared. All of the 1000 SSD particle simulations started with |
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the same configuration, and the only difference was the method used to |
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handle orientational motion. At time steps of 0.1 and 0.5 fs, both |
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methods for propagating the orientational degrees of freedom conserve |
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energy fairly well, with the quaternion method showing a slight energy |
| 305 |
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drift over time in the 0.5 fs time step simulation. At time steps of 1 |
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and 2 fs, the energy conservation benefits of the {\sc dlm} method are |
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clearly demonstrated. Thus, while maintaining the same degree of |
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energy conservation, one can take considerably longer time steps, |
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> |
leading to an overall reduction in computation time. |
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|
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Energy drift in the simulations using {\sc dlm} integration was unnoticeable |
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for time steps up to 3 fs. A slight energy drift on the order of 0.012 |
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kcal/mol per nanosecond was observed at a time step of 4 fs, and as |
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expected, this drift increases dramatically with increasing time |
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step. To insure accuracy in our microcanonical simulations, time steps |
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were set at 2 fs and kept at this value for constant pressure |
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simulations as well. |
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Energy drift in the simulations using {\sc dlm} integration was |
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unnoticeable for time steps up to 3 fs. A slight energy drift on the |
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order of 0.012 kcal/mol per nanosecond was observed at a time step of |
| 314 |
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4 fs, and as expected, this drift increases dramatically with |
| 315 |
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increasing time step. To insure accuracy in our microcanonical |
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simulations, time steps were set at 2 fs and kept at this value for |
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constant pressure simulations as well. |
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|
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Proton-disordered ice crystals in both the $I_h$ and $I_c$ lattices |
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were generated as starting points for all simulations. The $I_h$ |
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crystals were formed by first arranging the centers of mass of the {\sc ssd} |
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particles into a ``hexagonal'' ice lattice of 1024 particles. Because |
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of the crystal structure of $I_h$ ice, the simulation box assumed an |
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orthorhombic shape with an edge length ratio of approximately |
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1.00$\times$1.06$\times$1.23. The particles were then allowed to |
| 326 |
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orient freely about fixed positions with angular momenta randomized at |
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400 K for varying times. The rotational temperature was then scaled |
| 328 |
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down in stages to slowly cool the crystals to 25 K. The particles were |
| 329 |
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then allowed to translate with fixed orientations at a constant |
| 330 |
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pressure of 1 atm for 50 ps at 25 K. Finally, all constraints were |
| 331 |
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removed and the ice crystals were allowed to equilibrate for 50 ps at |
| 332 |
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25 K and a constant pressure of 1 atm. This procedure resulted in |
| 333 |
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structurally stable $I_h$ ice crystals that obey the Bernal-Fowler |
| 321 |
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crystals were formed by first arranging the centers of mass of the |
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SSD particles into a ``hexagonal'' ice lattice of 1024 |
| 323 |
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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 |
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ps at 25 K and a constant pressure of 1 atm. This procedure resulted |
| 333 |
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in structurally stable $I_h$ ice crystals that obey the Bernal-Fowler |
| 334 |
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rules.\cite{Bernal33,Rahman72} This method was also utilized in the |
| 335 |
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making of diamond lattice $I_c$ ice crystals, with each cubic |
| 336 |
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simulation box consisting of either 512 or 1000 particles. Only |
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|
| 358 |
|
\subsection{Density Behavior} |
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|
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Our initial simulations focused on the original {\sc ssd} water model, and |
| 361 |
< |
an average density versus temperature plot is shown in figure |
| 360 |
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Our initial simulations focused on the original SSD water model, |
| 361 |
> |
and an average density versus temperature plot is shown in figure |
| 362 |
|
\ref{dense1}. Note that the density maximum when using a reaction |
| 363 |
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field appears between 255 and 265 K. There were smaller fluctuations |
| 364 |
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in the density at 260 K than at either 255 or 265, so we report this |
| 371 |
|
\begin{figure} |
| 372 |
|
\begin{center} |
| 373 |
|
\epsfxsize=6in |
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< |
\epsfbox{denseSSD.eps} |
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> |
\epsfbox{denseSSDnew.eps} |
| 375 |
|
\caption{Density versus temperature for TIP4P [Ref. \citen{Jorgensen98b}], |
| 376 |
< |
TIP3P [Ref. \citen{Jorgensen98b}], SPC/E [Ref. \citen{Clancy94}], {\sc ssd} |
| 377 |
< |
without Reaction Field, {\sc ssd}, and experiment [Ref. \citen{CRC80}]. The |
| 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 {\sc ssd} |
| 380 |
< |
model were what prompted the original reparameterization of {\sc ssd1} |
| 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 |
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\label{dense1} |
| 383 |
|
\end{center} |
| 384 |
|
\end{figure} |
| 385 |
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|
| 386 |
< |
The density maximum for {\sc 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 |
| 386 |
> |
The density maximum for SSD compares quite favorably to other |
| 387 |
> |
simple water models. Figure \ref{dense1} also shows calculated |
| 388 |
> |
densities of several other models and experiment obtained from other |
| 389 |
|
sources.\cite{Jorgensen98b,Clancy94,CRC80} Of the listed simple water |
| 390 |
< |
models, {\sc ssd} has a temperature closest to the experimentally observed |
| 391 |
< |
density maximum. Of the {\it charge-based} models in |
| 390 |
> |
models, SSD has a temperature closest to the experimentally |
| 391 |
> |
observed density maximum. Of the {\it charge-based} models in |
| 392 |
|
Fig. \ref{dense1}, TIP4P has a density maximum behavior most like that |
| 393 |
< |
seen in {\sc ssd}. Though not included in this plot, it is useful |
| 394 |
< |
to note that TIP5P has a density maximum nearly identical to the |
| 393 |
> |
seen in SSD. Though not included in this plot, it is useful to |
| 394 |
> |
note that TIP5P has a density maximum nearly identical to the |
| 395 |
|
experimentally measured temperature. |
| 396 |
|
|
| 397 |
|
It has been observed that liquid state densities in water are |
| 398 |
|
dependent on the cutoff radius used both with and without the use of |
| 399 |
|
reaction field.\cite{Berendsen98} In order to address the possible |
| 400 |
|
effect of cutoff radius, simulations were performed with a dipolar |
| 401 |
< |
cutoff radius of 12.0 \AA\ to complement the previous {\sc 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 {\sc 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. |
| 401 |
> |
cutoff radius of 12.0 \AA\ to complement the previous SSD |
| 402 |
> |
simulations, all performed with a cutoff of 9.0 \AA. All of the |
| 403 |
> |
resulting densities overlapped within error and showed no significant |
| 404 |
> |
trend toward lower or higher densities as a function of cutoff radius, |
| 405 |
> |
for simulations both with and without reaction field. These results |
| 406 |
> |
indicate that there is no major benefit in choosing a longer cutoff |
| 407 |
> |
radius in simulations using SSD. This is advantageous in that |
| 408 |
> |
the use of a longer cutoff radius results in a significant increase in |
| 409 |
> |
the time required to obtain a single trajectory. |
| 410 |
|
|
| 411 |
|
The key feature to recognize in figure \ref{dense1} is the density |
| 412 |
< |
scaling of {\sc ssd} relative to other common models at any given |
| 413 |
< |
temperature. {\sc 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 |
| 412 |
> |
scaling of SSD relative to other common models at any given |
| 413 |
> |
temperature. SSD assumes a lower density than any of the other |
| 414 |
> |
listed models at the same pressure, behavior which is especially |
| 415 |
> |
apparent at temperatures greater than 300 K. Lower than expected |
| 416 |
> |
densities have been observed for other systems using a reaction field |
| 417 |
> |
for long-range electrostatic interactions, so the most likely reason |
| 418 |
> |
for the significantly lower densities seen in these simulations is the |
| 419 |
|
presence of the reaction field.\cite{Berendsen98,Nezbeda02} In order |
| 420 |
|
to test the effect of the reaction field on the density of the |
| 421 |
|
systems, the simulations were repeated without a reaction field |
| 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 {\sc ssd} simulations using reaction field, |
| 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 |
| 432 |
|
reaction field, the density around 300 K is still significantly lower |
| 433 |
|
than experiment and comparable water models. This anomalous behavior |
| 434 |
|
was what lead Tan {\it et al.} to recently reparameterize |
| 435 |
< |
{\sc ssd}.\cite{Ichiye03} Throughout the remainder of the paper our |
| 436 |
< |
reparamaterizations of {\sc ssd} will be compared with their newer {\sc ssd1} |
| 435 |
> |
SSD.\cite{Ichiye03} Throughout the remainder of the paper our |
| 436 |
> |
reparamaterizations of SSD will be compared with their newer SSD1 |
| 437 |
|
model. |
| 438 |
|
|
| 439 |
|
\subsection{Transport Behavior} |
| 457 |
|
\epsfxsize=6in |
| 458 |
|
\epsfbox{betterDiffuse.epsi} |
| 459 |
|
\caption{Average self-diffusion constant as a function of temperature for |
| 460 |
< |
{\sc ssd}, SPC/E [Ref. \citen{Clancy94}], and TIP5P |
| 460 |
> |
SSD, SPC/E [Ref. \citen{Clancy94}], and TIP5P |
| 461 |
|
[Ref. \citen{Jorgensen01}] compared with experimental data |
| 462 |
|
[Refs. \citen{Gillen72} and \citen{Holz00}]. Of the three water models |
| 463 |
< |
shown, {\sc ssd} has the least deviation from the experimental values. The |
| 464 |
< |
rapidly increasing diffusion constants for TIP5P and {\sc ssd} correspond to |
| 463 |
> |
shown, SSD has the least deviation from the experimental values. The |
| 464 |
> |
rapidly increasing diffusion constants for TIP5P and SSD correspond to |
| 465 |
|
significant decreases in density at the higher temperatures.} |
| 466 |
|
\label{diffuse} |
| 467 |
|
\end{center} |
| 468 |
|
\end{figure} |
| 469 |
|
|
| 470 |
|
The observed values for the diffusion constant point out one of the |
| 471 |
< |
strengths of the {\sc ssd} model. Of the three models shown, the {\sc ssd} model |
| 471 |
> |
strengths of the SSD model. Of the three models shown, the SSD model |
| 472 |
|
has the most accurate depiction of self-diffusion in both the |
| 473 |
|
supercooled and liquid regimes. SPC/E does a respectable job by |
| 474 |
|
reproducing values similar to experiment around 290 K; however, it |
| 475 |
|
deviates at both higher and lower temperatures, failing to predict the |
| 476 |
< |
correct thermal trend. TIP5P and {\sc ssd} both start off low at colder |
| 476 |
> |
correct thermal trend. TIP5P and SSD both start off low at colder |
| 477 |
|
temperatures and tend to diffuse too rapidly at higher temperatures. |
| 478 |
|
This behavior at higher temperatures is not particularly surprising |
| 479 |
< |
since the densities of both TIP5P and {\sc ssd} are lower than experimental |
| 479 |
> |
since the densities of both TIP5P and SSD are lower than experimental |
| 480 |
|
water densities at higher temperatures. When calculating the |
| 481 |
< |
diffusion coefficients for {\sc ssd} at experimental densities (instead of |
| 482 |
< |
the densities from the NPT simulations), the resulting values fall |
| 483 |
< |
more in line with experiment at these temperatures. |
| 481 |
> |
diffusion coefficients for SSD at experimental densities |
| 482 |
> |
(instead of the densities from the NPT simulations), the resulting |
| 483 |
> |
values fall more in line with experiment at these temperatures. |
| 484 |
|
|
| 485 |
|
\subsection{Structural Changes and Characterization} |
| 486 |
|
|
| 509 |
|
\epsfxsize=6in |
| 510 |
|
\epsfbox{fullContours.eps} |
| 511 |
|
\caption{Contour plots of 2D angular pair correlation functions for |
| 512 |
< |
512 {\sc ssd} molecules at 100 K (A \& B) and 300 K (C \& D). Dark areas |
| 512 |
> |
512 SSD molecules at 100 K (A \& B) and 300 K (C \& D). Dark areas |
| 513 |
|
signify regions of enhanced density while light areas signify |
| 514 |
|
depletion relative to the bulk density. White areas have pair |
| 515 |
|
correlation values below 0.5 and black areas have values above 1.5.} |
| 578 |
|
since the second solvation shell would still be shifted too far |
| 579 |
|
out. In addition, this would have an even more detrimental effect on |
| 580 |
|
the system densities, leading to a liquid with a more open structure |
| 581 |
< |
and a density considerably lower than the already low {\sc ssd} density. A |
| 582 |
< |
better correction would be to include the quadrupole-quadrupole |
| 583 |
< |
interactions for the water particles outside of the first solvation |
| 584 |
< |
shell, but this would remove the simplicity and speed advantage of |
| 585 |
< |
{\sc ssd}. |
| 581 |
> |
and a density considerably lower than the already low SSD |
| 582 |
> |
density. A better correction would be to include the |
| 583 |
> |
quadrupole-quadrupole interactions for the water particles outside of |
| 584 |
> |
the first solvation shell, but this would remove the simplicity and |
| 585 |
> |
speed advantage of SSD. |
| 586 |
|
|
| 587 |
< |
\subsection{Adjusted Potentials: {\sc ssd/rf} and {\sc ssd/e}} |
| 587 |
> |
\subsection{Adjusted Potentials: SSD/RF and SSD/E} |
| 588 |
|
|
| 589 |
< |
The propensity of {\sc ssd} to adopt lower than expected densities under |
| 589 |
> |
The propensity of SSD to adopt lower than expected densities under |
| 590 |
|
varying conditions is troubling, especially at higher temperatures. In |
| 591 |
|
order to correct this model for use with a reaction field, it is |
| 592 |
|
necessary to adjust the force field parameters for the primary |
| 602 |
|
function cutoffs ($r_l$, $r_u$ and $r_l^\prime$, $r_u^\prime$ |
| 603 |
|
respectively). The results of the reparameterizations are shown in |
| 604 |
|
table \ref{params}. We are calling these reparameterizations the Soft |
| 605 |
< |
Sticky Dipole / Reaction Field ({\sc ssd/rf} - for use with a reaction |
| 606 |
< |
field) and Soft Sticky Dipole Extended ({\sc ssd/e} - an attempt to improve |
| 605 |
> |
Sticky Dipole / Reaction Field (SSD/RF - for use with a reaction |
| 606 |
> |
field) and Soft Sticky Dipole Extended (SSD/E - an attempt to improve |
| 607 |
|
the liquid structure in simulations without a long-range correction). |
| 608 |
|
|
| 609 |
|
\begin{table} |
| 611 |
|
\caption{Parameters for the original and adjusted models} |
| 612 |
|
\begin{tabular}{ l c c c c } |
| 613 |
|
\hline \\[-3mm] |
| 614 |
< |
\ \ \ Parameters\ \ \ & \ \ \ {\sc ssd} [Ref. \citen{Ichiye96}] \ \ \ |
| 615 |
< |
& \ {\sc ssd1} [Ref. \citen{Ichiye03}]\ \ & \ {\sc ssd/e}\ \ & \ {\sc ssd/rf} \\ |
| 614 |
> |
\ \ \ Parameters\ \ \ & \ \ \ SSD [Ref. \citen{Ichiye96}] \ \ \ |
| 615 |
> |
& \ SSD1 [Ref. \citen{Ichiye03}]\ \ & \ SSD/E\ \ & \ SSD/RF \\ |
| 616 |
|
\hline \\[-3mm] |
| 617 |
|
\ \ \ $\sigma$ (\AA) & 3.051 & 3.016 & 3.035 & 3.019\\ |
| 618 |
|
\ \ \ $\epsilon$ (kcal/mol) & 0.152 & 0.152 & 0.152 & 0.152\\ |
| 632 |
|
\begin{center} |
| 633 |
|
\epsfxsize=5in |
| 634 |
|
\epsfbox{GofRCompare.epsi} |
| 635 |
< |
\caption{Plots comparing experiment [Ref. \citen{Head-Gordon00_1}] with {\sc ssd/e} |
| 636 |
< |
and {\sc ssd1} without reaction field (top), as well as {\sc ssd/rf} and {\sc ssd1} with |
| 637 |
< |
reaction field turned on (bottom). The insets show the respective |
| 638 |
< |
first peaks in detail. Note how the changes in parameters have lowered |
| 639 |
< |
and broadened the first peak of {\sc ssd/e} and {\sc ssd/rf}.} |
| 635 |
> |
\caption{Plots comparing experiment [Ref. \citen{Head-Gordon00_1}] with |
| 636 |
> |
SSD/E and SSD1 without reaction field (top), as well as |
| 637 |
> |
SSD/RF and SSD1 with reaction field turned on |
| 638 |
> |
(bottom). The insets show the respective first peaks in detail. Note |
| 639 |
> |
how the changes in parameters have lowered and broadened the first |
| 640 |
> |
peak of SSD/E and SSD/RF.} |
| 641 |
|
\label{grcompare} |
| 642 |
|
\end{center} |
| 643 |
|
\end{figure} |
| 647 |
|
\epsfxsize=6in |
| 648 |
|
\epsfbox{dualsticky_bw.eps} |
| 649 |
|
\caption{Positive and negative isosurfaces of the sticky potential for |
| 650 |
< |
{\sc ssd1} (left) and {\sc ssd/e} \& {\sc ssd/rf} (right). Light areas correspond to the |
| 651 |
< |
tetrahedral attractive component, and darker areas correspond to the |
| 652 |
< |
dipolar repulsive component.} |
| 650 |
> |
SSD1 (left) and SSD/E \& SSD/RF (right). Light areas |
| 651 |
> |
correspond to the tetrahedral attractive component, and darker areas |
| 652 |
> |
correspond to the dipolar repulsive component.} |
| 653 |
|
\label{isosurface} |
| 654 |
|
\end{center} |
| 655 |
|
\end{figure} |
| 656 |
|
|
| 657 |
< |
In the original paper detailing the development of {\sc ssd}, Liu and Ichiye |
| 657 |
> |
In the original paper detailing the development of SSD, Liu and Ichiye |
| 658 |
|
placed particular emphasis on an accurate description of the first |
| 659 |
|
solvation shell. This resulted in a somewhat tall and narrow first |
| 660 |
|
peak in $g(r)$ that integrated to give similar coordination numbers to |
| 661 |
|
the experimental data obtained by Soper and |
| 662 |
|
Phillips.\cite{Ichiye96,Soper86} New experimental x-ray scattering |
| 663 |
|
data from the Head-Gordon lab indicates a slightly lower and shifted |
| 664 |
< |
first peak in the g$_\mathrm{OO}(r)$, so our adjustments to {\sc ssd} were |
| 664 |
> |
first peak in the g$_\mathrm{OO}(r)$, so our adjustments to SSD were |
| 665 |
|
made after taking into consideration the new experimental |
| 666 |
|
findings.\cite{Head-Gordon00_1} Figure \ref{grcompare} shows the |
| 667 |
|
relocation of the first peak of the oxygen-oxygen $g(r)$ by comparing |
| 668 |
< |
the revised {\sc ssd} model ({\sc ssd1}), {\sc ssd/e}, and {\sc ssd/rf} to the new |
| 668 |
> |
the revised SSD model (SSD1), SSD/E, and SSD/RF to the new |
| 669 |
|
experimental results. Both modified water models have shorter peaks |
| 670 |
|
that match more closely to the experimental peak (as seen in the |
| 671 |
|
insets of figure \ref{grcompare}). This structural alteration was |
| 678 |
|
see how altering the cutoffs changes the repulsive and attractive |
| 679 |
|
character of the particles. With a reduced repulsive surface (darker |
| 680 |
|
region), the particles can move closer to one another, increasing the |
| 681 |
< |
density for the overall system. This change in interaction cutoff also |
| 682 |
< |
results in a more gradual orientational motion by allowing the |
| 681 |
> |
density for the overall system. This change in interaction cutoff |
| 682 |
> |
also results in a more gradual orientational motion by allowing the |
| 683 |
|
particles to maintain preferred dipolar arrangements before they begin |
| 684 |
|
to feel the pull of the tetrahedral restructuring. As the particles |
| 685 |
|
move closer together, the dipolar repulsion term becomes active and |
| 686 |
|
excludes unphysical nearest-neighbor arrangements. This compares with |
| 687 |
< |
how {\sc ssd} and {\sc ssd1} exclude preferred dipole alignments before the |
| 687 |
> |
how SSD and SSD1 exclude preferred dipole alignments before the |
| 688 |
|
particles feel the pull of the ``hydrogen bonds''. Aside from |
| 689 |
|
improving the shape of the first peak in the g(\emph{r}), this |
| 690 |
|
modification improves the densities considerably by allowing the |
| 695 |
|
improves the densities, these changes alone are insufficient to bring |
| 696 |
|
the system densities up to the values observed experimentally. To |
| 697 |
|
further increase the densities, the dipole moments were increased in |
| 698 |
< |
both of our adjusted models. Since {\sc ssd} is a dipole based model, the |
| 699 |
< |
structure and transport are very sensitive to changes in the dipole |
| 700 |
< |
moment. The original {\sc ssd} simply used the dipole moment calculated from |
| 701 |
< |
the TIP3P water model, which at 2.35 D is significantly greater than |
| 702 |
< |
the experimental gas phase value of 1.84 D. The larger dipole moment |
| 703 |
< |
is a more realistic value and improves the dielectric properties of |
| 704 |
< |
the fluid. Both theoretical and experimental measurements indicate a |
| 705 |
< |
liquid phase dipole moment ranging from 2.4 D to values as high as |
| 706 |
< |
3.11 D, providing a substantial range of reasonable values for a |
| 707 |
< |
dipole moment.\cite{Sprik91,Kusalik02,Badyal00,Barriol64} Moderately |
| 708 |
< |
increasing the dipole moments to 2.42 and 2.48 D for {\sc ssd/e} and {\sc ssd/rf}, |
| 709 |
< |
respectively, leads to significant changes in the density and |
| 710 |
< |
transport of the water models. |
| 698 |
> |
both of our adjusted models. Since SSD is a dipole based model, |
| 699 |
> |
the structure and transport are very sensitive to changes in the |
| 700 |
> |
dipole moment. The original SSD simply used the dipole moment |
| 701 |
> |
calculated from the TIP3P water model, which at 2.35 D is |
| 702 |
> |
significantly greater than the experimental gas phase value of 1.84 |
| 703 |
> |
D. The larger dipole moment is a more realistic value and improves the |
| 704 |
> |
dielectric properties of the fluid. Both theoretical and experimental |
| 705 |
> |
measurements indicate a liquid phase dipole moment ranging from 2.4 D |
| 706 |
> |
to values as high as 3.11 D, providing a substantial range of |
| 707 |
> |
reasonable values for a dipole |
| 708 |
> |
moment.\cite{Sprik91,Kusalik02,Badyal00,Barriol64} Moderately |
| 709 |
> |
increasing the dipole moments to 2.42 and 2.48 D for SSD/E and |
| 710 |
> |
SSD/RF, respectively, leads to significant changes in the |
| 711 |
> |
density and transport of the water models. |
| 712 |
|
|
| 713 |
|
In order to demonstrate the benefits of these reparameterizations, a |
| 714 |
|
series of NPT and NVE simulations were performed to probe the density |
| 715 |
|
and transport properties of the adapted models and compare the results |
| 716 |
< |
to the original {\sc ssd} model. This comparison involved full NPT melting |
| 717 |
< |
sequences for both {\sc ssd/e} and {\sc ssd/rf}, as well as NVE transport |
| 716 |
> |
to the original SSD model. This comparison involved full NPT melting |
| 717 |
> |
sequences for both SSD/E and SSD/RF, as well as NVE transport |
| 718 |
|
calculations at the calculated self-consistent densities. Again, the |
| 719 |
|
results are obtained from five separate simulations of 1024 particle |
| 720 |
|
systems, and the melting sequences were started from different ice |
| 729 |
|
\begin{center} |
| 730 |
|
\epsfxsize=6in |
| 731 |
|
\epsfbox{ssdeDense.epsi} |
| 732 |
< |
\caption{Comparison of densities calculated with {\sc ssd/e} to {\sc ssd1} without a |
| 733 |
< |
reaction field, TIP3P [Ref. \citen{Jorgensen98b}], TIP5P |
| 734 |
< |
[Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}] and |
| 732 |
> |
\caption{Comparison of densities calculated with SSD/E to |
| 733 |
> |
SSD1 without a reaction field, TIP3P [Ref. \citen{Jorgensen98b}], |
| 734 |
> |
TIP5P [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}] and |
| 735 |
|
experiment [Ref. \citen{CRC80}]. The window shows a expansion around |
| 736 |
|
300 K with error bars included to clarify this region of |
| 737 |
< |
interest. Note that both {\sc ssd1} and {\sc ssd/e} show good agreement with |
| 737 |
> |
interest. Note that both SSD1 and SSD/E show good agreement with |
| 738 |
|
experiment when the long-range correction is neglected.} |
| 739 |
|
\label{ssdedense} |
| 740 |
|
\end{center} |
| 741 |
|
\end{figure} |
| 742 |
|
|
| 743 |
< |
Fig. \ref{ssdedense} shows the density profile for the {\sc ssd/e} model |
| 744 |
< |
in comparison to {\sc ssd1} without a reaction field, other common water |
| 745 |
< |
models, and experimental results. The calculated densities for both |
| 746 |
< |
{\sc ssd/e} and {\sc ssd1} have increased significantly over the original {\sc ssd} |
| 747 |
< |
model (see fig. \ref{dense1}) and are in better agreement with the |
| 748 |
< |
experimental values. At 298 K, the densities of {\sc ssd/e} and {\sc ssd1} without |
| 743 |
> |
Fig. \ref{ssdedense} shows the density profile for the SSD/E |
| 744 |
> |
model in comparison to SSD1 without a reaction field, other |
| 745 |
> |
common water models, and experimental results. The calculated |
| 746 |
> |
densities for both SSD/E and SSD1 have increased |
| 747 |
> |
significantly over the original SSD model (see |
| 748 |
> |
fig. \ref{dense1}) and are in better agreement with the experimental |
| 749 |
> |
values. At 298 K, the densities of SSD/E and SSD1 without |
| 750 |
|
a long-range correction are 0.996$\pm$0.001 g/cm$^3$ and |
| 751 |
|
0.999$\pm$0.001 g/cm$^3$ respectively. These both compare well with |
| 752 |
|
the experimental value of 0.997 g/cm$^3$, and they are considerably |
| 753 |
< |
better than the {\sc ssd} value of 0.967$\pm$0.003 g/cm$^3$. The changes to |
| 754 |
< |
the dipole moment and sticky switching functions have improved the |
| 755 |
< |
structuring of the liquid (as seen in figure \ref{grcompare}, but they |
| 756 |
< |
have shifted the density maximum to much lower temperatures. This |
| 757 |
< |
comes about via an increase in the liquid disorder through the |
| 758 |
< |
weakening of the sticky potential and strengthening of the dipolar |
| 759 |
< |
character. However, this increasing disorder in the {\sc ssd/e} model has |
| 760 |
< |
little effect on the melting transition. By monitoring $C_p$ |
| 761 |
< |
throughout these simulations, the melting transition for {\sc ssd/e} was |
| 762 |
< |
shown to occur at 235 K. The same transition temperature observed |
| 763 |
< |
with {\sc ssd} and {\sc ssd1}. |
| 753 |
> |
better than the SSD value of 0.967$\pm$0.003 g/cm$^3$. The |
| 754 |
> |
changes to the dipole moment and sticky switching functions have |
| 755 |
> |
improved the structuring of the liquid (as seen in figure |
| 756 |
> |
\ref{grcompare}, but they have shifted the density maximum to much |
| 757 |
> |
lower temperatures. This comes about via an increase in the liquid |
| 758 |
> |
disorder through the weakening of the sticky potential and |
| 759 |
> |
strengthening of the dipolar character. However, this increasing |
| 760 |
> |
disorder in the SSD/E model has little effect on the melting |
| 761 |
> |
transition. By monitoring $C_p$ throughout these simulations, the |
| 762 |
> |
melting transition for SSD/E was shown to occur at 235 K. The |
| 763 |
> |
same transition temperature observed with SSD and SSD1. |
| 764 |
|
|
| 765 |
|
\begin{figure} |
| 766 |
|
\begin{center} |
| 767 |
|
\epsfxsize=6in |
| 768 |
|
\epsfbox{ssdrfDense.epsi} |
| 769 |
< |
\caption{Comparison of densities calculated with {\sc ssd/rf} to {\sc ssd1} with a |
| 770 |
< |
reaction field, TIP3P [Ref. \citen{Jorgensen98b}], TIP5P |
| 771 |
< |
[Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}], and |
| 769 |
> |
\caption{Comparison of densities calculated with SSD/RF to |
| 770 |
> |
SSD1 with a reaction field, TIP3P [Ref. \citen{Jorgensen98b}], |
| 771 |
> |
TIP5P [Ref. \citen{Jorgensen00}], SPC/E [Ref. \citen{Clancy94}], and |
| 772 |
|
experiment [Ref. \citen{CRC80}]. The inset shows the necessity of |
| 773 |
|
reparameterization when utilizing a reaction field long-ranged |
| 774 |
< |
correction - {\sc ssd/rf} provides significantly more accurate densities |
| 775 |
< |
than {\sc ssd1} when performing room temperature simulations.} |
| 774 |
> |
correction - SSD/RF provides significantly more accurate |
| 775 |
> |
densities than SSD1 when performing room temperature |
| 776 |
> |
simulations.} |
| 777 |
|
\label{ssdrfdense} |
| 778 |
|
\end{center} |
| 779 |
|
\end{figure} |
| 780 |
|
|
| 781 |
|
Including the reaction field long-range correction in the simulations |
| 782 |
|
results in a more interesting comparison. A density profile including |
| 783 |
< |
{\sc ssd/rf} and {\sc ssd1} with an active reaction field is shown in figure |
| 783 |
> |
SSD/RF and SSD1 with an active reaction field is shown in figure |
| 784 |
|
\ref{ssdrfdense}. As observed in the simulations without a reaction |
| 785 |
< |
field, the densities of {\sc ssd/rf} and {\sc ssd1} show a dramatic increase over |
| 786 |
< |
normal {\sc ssd} (see figure \ref{dense1}). At 298 K, {\sc ssd/rf} has a density |
| 785 |
> |
field, the densities of SSD/RF and SSD1 show a dramatic increase over |
| 786 |
> |
normal SSD (see figure \ref{dense1}). At 298 K, SSD/RF has a density |
| 787 |
|
of 0.997$\pm$0.001 g/cm$^3$, directly in line with experiment and |
| 788 |
< |
considerably better than the original {\sc ssd} value of 0.941$\pm$0.001 |
| 789 |
< |
g/cm$^3$ and the {\sc ssd1} value of 0.972$\pm$0.002 g/cm$^3$. These results |
| 788 |
> |
considerably better than the original SSD value of 0.941$\pm$0.001 |
| 789 |
> |
g/cm$^3$ and the SSD1 value of 0.972$\pm$0.002 g/cm$^3$. These results |
| 790 |
|
further emphasize the importance of reparameterization in order to |
| 791 |
|
model the density properly under different simulation conditions. |
| 792 |
|
Again, these changes have only a minor effect on the melting point, |
| 793 |
< |
which observed at 245 K for {\sc ssd/rf}, is identical to {\sc ssd} and only 5 K |
| 794 |
< |
lower than {\sc ssd1} with a reaction field. Additionally, the difference in |
| 795 |
< |
density maxima is not as extreme, with {\sc ssd/rf} showing a density |
| 793 |
> |
which observed at 245 K for SSD/RF, is identical to SSD and only 5 K |
| 794 |
> |
lower than SSD1 with a reaction field. Additionally, the difference in |
| 795 |
> |
density maxima is not as extreme, with SSD/RF showing a density |
| 796 |
|
maximum at 255 K, fairly close to the density maxima of 260 K and 265 |
| 797 |
< |
K, shown by {\sc ssd} and {\sc ssd1} respectively. |
| 797 |
> |
K, shown by SSD and SSD1 respectively. |
| 798 |
|
|
| 799 |
|
\begin{figure} |
| 800 |
|
\begin{center} |
| 801 |
|
\epsfxsize=6in |
| 802 |
|
\epsfbox{ssdeDiffuse.epsi} |
| 803 |
< |
\caption{The diffusion constants calculated from {\sc ssd/e} and {\sc ssd1} (both |
| 804 |
< |
without a reaction field) along with experimental results |
| 803 |
> |
\caption{The diffusion constants calculated from SSD/E and |
| 804 |
> |
SSD1 (both without a reaction field) along with experimental results |
| 805 |
|
[Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations were |
| 806 |
|
performed at the average densities observed in the 1 atm NPT |
| 807 |
< |
simulations for the respective models. {\sc ssd/e} is slightly more mobile |
| 807 |
> |
simulations for the respective models. SSD/E is slightly more mobile |
| 808 |
|
than experiment at all of the temperatures, but it is closer to |
| 809 |
< |
experiment at biologically relevant temperatures than {\sc ssd1} without a |
| 809 |
> |
experiment at biologically relevant temperatures than SSD1 without a |
| 810 |
|
long-range correction.} |
| 811 |
|
\label{ssdediffuse} |
| 812 |
|
\end{center} |
| 813 |
|
\end{figure} |
| 814 |
|
|
| 815 |
< |
The reparameterization of the {\sc ssd} water model, both for use with and |
| 815 |
> |
The reparameterization of the SSD water model, both for use with and |
| 816 |
|
without an applied long-range correction, brought the densities up to |
| 817 |
|
what is expected for simulating liquid water. In addition to improving |
| 818 |
< |
the densities, it is important that the diffusive behavior of {\sc ssd} be |
| 818 |
> |
the densities, it is important that the diffusive behavior of SSD be |
| 819 |
|
maintained or improved. Figure \ref{ssdediffuse} compares the |
| 820 |
< |
temperature dependence of the diffusion constant of {\sc ssd/e} to {\sc ssd1} |
| 820 |
> |
temperature dependence of the diffusion constant of SSD/E to SSD1 |
| 821 |
|
without an active reaction field at the densities calculated from |
| 822 |
|
their respective NPT simulations at 1 atm. The diffusion constant for |
| 823 |
< |
{\sc ssd/e} is consistently higher than experiment, while {\sc ssd1} remains lower |
| 823 |
> |
SSD/E is consistently higher than experiment, while SSD1 remains lower |
| 824 |
|
than experiment until relatively high temperatures (around 360 |
| 825 |
|
K). Both models follow the shape of the experimental curve well below |
| 826 |
|
300 K but tend to diffuse too rapidly at higher temperatures, as seen |
| 827 |
< |
in {\sc ssd1}'s crossing above 360 K. This increasing diffusion relative to |
| 827 |
> |
in SSD1's crossing above 360 K. This increasing diffusion relative to |
| 828 |
|
the experimental values is caused by the rapidly decreasing system |
| 829 |
< |
density with increasing temperature. Both {\sc ssd1} and {\sc ssd/e} show this |
| 829 |
> |
density with increasing temperature. Both SSD1 and SSD/E show this |
| 830 |
|
deviation in particle mobility, but this trend has different |
| 831 |
< |
implications on the diffusive behavior of the models. While {\sc ssd1} |
| 831 |
> |
implications on the diffusive behavior of the models. While SSD1 |
| 832 |
|
shows more experimentally accurate diffusive behavior in the high |
| 833 |
< |
temperature regimes, {\sc ssd/e} shows more accurate behavior in the |
| 833 |
> |
temperature regimes, SSD/E shows more accurate behavior in the |
| 834 |
|
supercooled and biologically relevant temperature ranges. Thus, the |
| 835 |
|
changes made to improve the liquid structure may have had an adverse |
| 836 |
|
affect on the density maximum, but they improve the transport behavior |
| 837 |
< |
of {\sc ssd/e} relative to {\sc ssd1} under the most commonly simulated |
| 837 |
> |
of SSD/E relative to SSD1 under the most commonly simulated |
| 838 |
|
conditions. |
| 839 |
|
|
| 840 |
|
\begin{figure} |
| 841 |
|
\begin{center} |
| 842 |
|
\epsfxsize=6in |
| 843 |
|
\epsfbox{ssdrfDiffuse.epsi} |
| 844 |
< |
\caption{The diffusion constants calculated from {\sc ssd/rf} and {\sc ssd1} (both |
| 845 |
< |
with an active reaction field) along with experimental results |
| 846 |
< |
[Refs. \citen{Gillen72} and \citen{Holz00}]. The NVE calculations were |
| 847 |
< |
performed at the average densities observed in the 1 atm NPT |
| 848 |
< |
simulations for both of the models. {\sc ssd/rf} simulates the diffusion of |
| 849 |
< |
water throughout this temperature range very well. The rapidly |
| 850 |
< |
increasing diffusion constants at high temperatures for both models |
| 851 |
< |
can be attributed to lower calculated densities than those observed in |
| 852 |
< |
experiment.} |
| 844 |
> |
\caption{The diffusion constants calculated from SSD/RF and |
| 845 |
> |
SSD1 (both with an active reaction field) along with |
| 846 |
> |
experimental results [Refs. \citen{Gillen72} and \citen{Holz00}]. The |
| 847 |
> |
NVE calculations were performed at the average densities observed in |
| 848 |
> |
the 1 atm NPT simulations for both of the models. SSD/RF |
| 849 |
> |
simulates the diffusion of water throughout this temperature range |
| 850 |
> |
very well. The rapidly increasing diffusion constants at high |
| 851 |
> |
temperatures for both models can be attributed to lower calculated |
| 852 |
> |
densities than those observed in experiment.} |
| 853 |
|
\label{ssdrfdiffuse} |
| 854 |
|
\end{center} |
| 855 |
|
\end{figure} |
| 856 |
|
|
| 857 |
< |
In figure \ref{ssdrfdiffuse}, the diffusion constants for {\sc ssd/rf} are |
| 858 |
< |
compared to {\sc ssd1} with an active reaction field. Note that {\sc ssd/rf} |
| 857 |
> |
In figure \ref{ssdrfdiffuse}, the diffusion constants for SSD/RF are |
| 858 |
> |
compared to SSD1 with an active reaction field. Note that SSD/RF |
| 859 |
|
tracks the experimental results quantitatively, identical within error |
| 860 |
|
throughout most of the temperature range shown and exhibiting only a |
| 861 |
< |
slight increasing trend at higher temperatures. {\sc ssd1} tends to diffuse |
| 861 |
> |
slight increasing trend at higher temperatures. SSD1 tends to diffuse |
| 862 |
|
more slowly at low temperatures and deviates to diffuse too rapidly at |
| 863 |
|
temperatures greater than 330 K. As stated above, this deviation away |
| 864 |
|
from the ideal trend is due to a rapid decrease in density at higher |
| 865 |
< |
temperatures. {\sc ssd/rf} does not suffer from this problem as much as {\sc ssd1} |
| 865 |
> |
temperatures. SSD/RF does not suffer from this problem as much as SSD1 |
| 866 |
|
because the calculated densities are closer to the experimental |
| 867 |
|
values. These results again emphasize the importance of careful |
| 868 |
|
reparameterization when using an altered long-range correction. |
| 875 |
|
experimental data at ambient conditions} |
| 876 |
|
\begin{tabular}{ l c c c c c } |
| 877 |
|
\hline \\[-3mm] |
| 878 |
< |
\ \ \ \ \ \ & \ \ \ {\sc ssd1} \ \ \ & \ {\sc ssd/e} \ \ \ & \ {\sc ssd1} (RF) \ \ |
| 879 |
< |
\ & \ {\sc ssd/rf} \ \ \ & \ Expt. \\ |
| 878 |
> |
\ \ \ \ \ \ & \ \ \ SSD1 \ \ \ & \ SSD/E \ \ \ & \ SSD1 (RF) \ \ |
| 879 |
> |
\ & \ SSD/RF \ \ \ & \ Expt. \\ |
| 880 |
|
\hline \\[-3mm] |
| 881 |
|
\ \ \ $\rho$ (g/cm$^3$) & 0.999 $\pm$0.001 & 0.996 $\pm$0.001 & 0.972 $\pm$0.002 & 0.997 $\pm$0.001 & 0.997 \\ |
| 882 |
|
\ \ \ $C_p$ (cal/mol K) & 28.80 $\pm$0.11 & 25.45 $\pm$0.09 & 28.28 $\pm$0.06 & 23.83 $\pm$0.16 & 17.98 \\ |
| 914 |
|
$a$ and $b$ are the radial locations of the minima following the first |
| 915 |
|
peak in g$_\text{OO}(r)$ or g$_\text{OH}(r)$ respectively. The number |
| 916 |
|
of hydrogen bonds stays relatively constant across all of the models, |
| 917 |
< |
but the coordination numbers of {\sc ssd/e} and {\sc ssd/rf} show an improvement |
| 918 |
< |
over {\sc ssd1}. This improvement is primarily due to extension of the |
| 919 |
< |
first solvation shell in the new parameter sets. Because $n_H$ and |
| 920 |
< |
$n_C$ are nearly identical in {\sc ssd1}, it appears that all molecules in |
| 921 |
< |
the first solvation shell are involved in hydrogen bonds. Since $n_H$ |
| 922 |
< |
and $n_C$ differ in the newly parameterized models, the orientations |
| 923 |
< |
in the first solvation shell are a bit more ``fluid''. Therefore {\sc ssd1} |
| 924 |
< |
overstructures the first solvation shell and our reparameterizations |
| 925 |
< |
have returned this shell to more realistic liquid-like behavior. |
| 917 |
> |
but the coordination numbers of SSD/E and SSD/RF show an |
| 918 |
> |
improvement over SSD1. This improvement is primarily due to |
| 919 |
> |
extension of the first solvation shell in the new parameter sets. |
| 920 |
> |
Because $n_H$ and $n_C$ are nearly identical in SSD1, it appears |
| 921 |
> |
that all molecules in the first solvation shell are involved in |
| 922 |
> |
hydrogen bonds. Since $n_H$ and $n_C$ differ in the newly |
| 923 |
> |
parameterized models, the orientations in the first solvation shell |
| 924 |
> |
are a bit more ``fluid''. Therefore SSD1 overstructures the |
| 925 |
> |
first solvation shell and our reparameterizations have returned this |
| 926 |
> |
shell to more realistic liquid-like behavior. |
| 927 |
|
|
| 928 |
|
The time constants for the orientational autocorrelation functions |
| 929 |
|
are also displayed in Table \ref{liquidproperties}. The dipolar |
| 948 |
|
\ref{liquidproperties} was calculated from the same NMR data in the |
| 949 |
|
fashion described in Ref. \citen{Krynicki66}. Similarly, $\tau_1$ was |
| 950 |
|
recomputed for 298 K from the data in Ref. \citen{Eisenberg69}. |
| 951 |
< |
Again, {\sc ssd/e} and {\sc ssd/rf} show improved behavior over {\sc ssd1}, both with |
| 951 |
> |
Again, SSD/E and SSD/RF show improved behavior over SSD1, both with |
| 952 |
|
and without an active reaction field. Turning on the reaction field |
| 953 |
< |
leads to much improved time constants for {\sc ssd1}; however, these results |
| 953 |
> |
leads to much improved time constants for SSD1; however, these results |
| 954 |
|
also include a corresponding decrease in system density. |
| 955 |
< |
Orientational relaxation times published in the original {\sc ssd} dynamics |
| 955 |
> |
Orientational relaxation times published in the original SSD dynamics |
| 956 |
|
papers are smaller than the values observed here, and this difference |
| 957 |
|
can be attributed to the use of the Ewald sum.\cite{Ichiye99} |
| 958 |
|
|
| 962 |
|
\begin{center} |
| 963 |
|
\epsfxsize=6in |
| 964 |
|
\epsfbox{icei_bw.eps} |
| 965 |
< |
\caption{The most stable crystal structure assumed by the {\sc ssd} family |
| 965 |
> |
\caption{The most stable crystal structure assumed by the SSD family |
| 966 |
|
of water models. We refer to this structure as Ice-{\it i} to |
| 967 |
|
indicate its origins in computer simulation. This image was taken of |
| 968 |
|
the (001) face of the crystal.} |
| 971 |
|
\end{figure} |
| 972 |
|
|
| 973 |
|
While performing a series of melting simulations on an early iteration |
| 974 |
< |
of {\sc ssd/e} not discussed in this paper, we observed recrystallization |
| 975 |
< |
into a novel structure not previously known for water. After melting |
| 976 |
< |
at 235 K, two of five systems underwent crystallization events near |
| 977 |
< |
245 K. The two systems remained crystalline up to 320 and 330 K, |
| 978 |
< |
respectively. The crystal exhibits an expanded zeolite-like structure |
| 979 |
< |
that does not correspond to any known form of ice. This appears to be |
| 980 |
< |
an artifact of the point dipolar models, so to distinguish it from the |
| 981 |
< |
experimentally observed forms of ice, we have denoted the structure |
| 974 |
> |
of SSD/E not discussed in this paper, we observed |
| 975 |
> |
recrystallization into a novel structure not previously known for |
| 976 |
> |
water. After melting at 235 K, two of five systems underwent |
| 977 |
> |
crystallization events near 245 K. The two systems remained |
| 978 |
> |
crystalline up to 320 and 330 K, respectively. The crystal exhibits |
| 979 |
> |
an expanded zeolite-like structure that does not correspond to any |
| 980 |
> |
known form of ice. This appears to be an artifact of the point |
| 981 |
> |
dipolar models, so to distinguish it from the experimentally observed |
| 982 |
> |
forms of ice, we have denoted the structure |
| 983 |
|
Ice-$\sqrt{\smash[b]{-\text{I}}}$ (Ice-{\it i}). A large enough |
| 984 |
|
portion of the sample crystallized that we have been able to obtain a |
| 985 |
|
near ideal crystal structure of Ice-{\it i}. Figure \ref{weirdice} |
| 994 |
|
favorable enough to stabilize an entire crystal generated around them. |
| 995 |
|
|
| 996 |
|
Initial simulations indicated that Ice-{\it i} is the preferred ice |
| 997 |
< |
structure for at least the {\sc ssd/e} model. To verify this, a |
| 998 |
< |
comparison was made between near ideal crystals of ice~$I_h$, |
| 999 |
< |
ice~$I_c$, and Ice-{\it i} at constant pressure with {\sc ssd/e}, {\sc |
| 1000 |
< |
ssd/rf}, and {\sc ssd1}. Near-ideal versions of the three types of |
| 1001 |
< |
crystals were cooled to 1 K, and enthalpies of formation of each were |
| 1002 |
< |
compared using all three water models. Enthalpies were estimated from |
| 1003 |
< |
the isobaric-isothermal simulations using $H=U+P_{\text ext}V$ where |
| 1004 |
< |
$P_{\text ext}$ is the applied pressure. A constant value of |
| 1005 |
< |
-60.158 kcal / mol has been added to place our zero for the |
| 1006 |
< |
enthalpies of formation for these systems at the traditional state |
| 1007 |
< |
(elemental forms at standard temperature and pressure). With every |
| 1008 |
< |
model in the {\sc ssd} family, Ice-{\it i} had the lowest calculated |
| 1002 |
< |
enthalpy of formation. |
| 997 |
> |
structure for at least the SSD/E model. To verify this, a comparison |
| 998 |
> |
was made between near ideal crystals of ice~$I_h$, ice~$I_c$, and |
| 999 |
> |
Ice-{\it i} at constant pressure with SSD/E, SSD/RF, and |
| 1000 |
> |
SSD1. Near-ideal versions of the three types of crystals were cooled |
| 1001 |
> |
to 1 K, and enthalpies of formation of each were compared using all |
| 1002 |
> |
three water models. Enthalpies were estimated from the |
| 1003 |
> |
isobaric-isothermal simulations using $H=U+P_{\text ext}V$ where |
| 1004 |
> |
$P_{\text ext}$ is the applied pressure. A constant value of -60.158 |
| 1005 |
> |
kcal / mol has been added to place our zero for the enthalpies of |
| 1006 |
> |
formation for these systems at the traditional state (elemental forms |
| 1007 |
> |
at standard temperature and pressure). With every model in the SSD |
| 1008 |
> |
family, Ice-{\it i} had the lowest calculated enthalpy of formation. |
| 1009 |
|
|
| 1010 |
|
\begin{table} |
| 1011 |
|
\begin{center} |
| 1012 |
|
\caption{Enthalpies of Formation (in kcal / mol) of the three crystal |
| 1013 |
< |
structures (at 1 K) exhibited by the {\sc ssd} family of water models} |
| 1013 |
> |
structures (at 1 K) exhibited by the SSD family of water models} |
| 1014 |
|
\begin{tabular}{ l c c c } |
| 1015 |
|
\hline \\[-3mm] |
| 1016 |
|
\ \ \ Water Model \ \ \ & \ \ \ Ice-$I_h$ \ \ \ & \ Ice-$I_c$\ \ & \ |
| 1017 |
|
Ice-{\it i} \\ |
| 1018 |
|
\hline \\[-3mm] |
| 1019 |
< |
\ \ \ {\sc ssd/e} & -12.286 & -12.292 & -13.590 \\ |
| 1020 |
< |
\ \ \ {\sc ssd/rf} & -12.935 & -12.917 & -14.022 \\ |
| 1021 |
< |
\ \ \ {\sc ssd1} & -12.496 & -12.411 & -13.417 \\ |
| 1022 |
< |
\ \ \ {\sc ssd1} (RF) & -12.504 & -12.411 & -13.134 \\ |
| 1019 |
> |
\ \ \ SSD/E & -72.444 & -72.450 & -73.748 \\ |
| 1020 |
> |
\ \ \ SSD/RF & -73.093 & -73.075 & -74.180 \\ |
| 1021 |
> |
\ \ \ SSD1 & -72.654 & -72.569 & -73.575 \\ |
| 1022 |
> |
\ \ \ SSD1 (RF) & -72.662 & -72.569 & -73.292 \\ |
| 1023 |
|
\end{tabular} |
| 1024 |
|
\label{iceenthalpy} |
| 1025 |
|
\end{center} |
| 1026 |
|
\end{table} |
| 1027 |
|
|
| 1028 |
|
In addition to these energetic comparisons, melting simulations were |
| 1029 |
< |
performed with ice-{\it i} as the initial configuration using {\sc ssd/e}, |
| 1030 |
< |
{\sc ssd/rf}, and {\sc ssd1} both with and without a reaction field. The melting |
| 1031 |
< |
transitions for both {\sc ssd/e} and {\sc ssd1} without reaction field occurred at |
| 1032 |
< |
temperature in excess of 375~K. {\sc ssd/rf} and {\sc ssd1} with a reaction field |
| 1029 |
> |
performed with ice-{\it i} as the initial configuration using SSD/E, |
| 1030 |
> |
SSD/RF, and SSD1 both with and without a reaction field. The melting |
| 1031 |
> |
transitions for both SSD/E and SSD1 without reaction field occurred at |
| 1032 |
> |
temperature in excess of 375~K. SSD/RF and SSD1 with a reaction field |
| 1033 |
|
showed more reasonable melting transitions near 325~K. These melting |
| 1034 |
< |
point observations clearly show that all of the {\sc ssd}-derived models |
| 1034 |
> |
point observations clearly show that all of the SSD-derived models |
| 1035 |
|
prefer the ice-{\it i} structure. |
| 1036 |
|
|
| 1037 |
|
\section{Conclusions} |
| 1038 |
|
|
| 1039 |
|
The density maximum and temperature dependence of the self-diffusion |
| 1040 |
< |
constant were studied for the {\sc ssd} water model, both with and without |
| 1041 |
< |
the use of reaction field, via a series of NPT and NVE |
| 1040 |
> |
constant were studied for the SSD water model, both with and |
| 1041 |
> |
without the use of reaction field, via a series of NPT and NVE |
| 1042 |
|
simulations. The constant pressure simulations showed a density |
| 1043 |
|
maximum near 260 K. In most cases, the calculated densities were |
| 1044 |
|
significantly lower than the densities obtained from other water |
| 1045 |
< |
models (and experiment). Analysis of self-diffusion showed {\sc ssd} to |
| 1046 |
< |
capture the transport properties of water well in both the liquid and |
| 1047 |
< |
supercooled liquid regimes. |
| 1045 |
> |
models (and experiment). Analysis of self-diffusion showed SSD |
| 1046 |
> |
to capture the transport properties of water well in both the liquid |
| 1047 |
> |
and supercooled liquid regimes. |
| 1048 |
|
|
| 1049 |
< |
In order to correct the density behavior, the original {\sc ssd} model was |
| 1050 |
< |
reparameterized for use both with and without a reaction field ({\sc ssd/rf} |
| 1051 |
< |
and {\sc ssd/e}), and comparisons were made with {\sc ssd1}, Ichiye's density |
| 1052 |
< |
corrected version of {\sc ssd}. Both models improve the liquid structure, |
| 1049 |
> |
In order to correct the density behavior, the original SSD model was |
| 1050 |
> |
reparameterized for use both with and without a reaction field (SSD/RF |
| 1051 |
> |
and SSD/E), and comparisons were made with SSD1, Ichiye's density |
| 1052 |
> |
corrected version of SSD. Both models improve the liquid structure, |
| 1053 |
|
densities, and diffusive properties under their respective simulation |
| 1054 |
|
conditions, indicating the necessity of reparameterization when |
| 1055 |
|
changing the method of calculating long-range electrostatic |
| 1058 |
|
simulations of biochemical systems. |
| 1059 |
|
|
| 1060 |
|
The existence of a novel low-density ice structure that is preferred |
| 1061 |
< |
by the {\sc ssd} family of water models is somewhat troubling, since liquid |
| 1062 |
< |
simulations on this family of water models at room temperature are |
| 1063 |
< |
effectively simulations of supercooled or metastable liquids. One |
| 1061 |
> |
by the SSD family of water models is somewhat troubling, since |
| 1062 |
> |
liquid simulations on this family of water models at room temperature |
| 1063 |
> |
are effectively simulations of supercooled or metastable liquids. One |
| 1064 |
|
way to destabilize this unphysical ice structure would be to make the |
| 1065 |
|
range of angles preferred by the attractive part of the sticky |
| 1066 |
|
potential much narrower. This would require extensive |
