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\section{\label{sec:SSD}Water Model: SSD and Derivatives} |
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|
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In the interest of computational efficiency, the native solvent used |
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in {\sc oopse} is the Soft Sticky Dipole (SSD) water model. SSD was |
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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} It consists of a single point dipole |
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with a Lennard-Jones core and a sticky potential that directs the |
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particles to assume the proper hydrogen bond orientation in the first |
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solvation shell. Thus, the interaction between two SSD water molecules |
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\emph{i} and \emph{j} 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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(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j)\ + |
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u_{ij}^{sp} |
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(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j), |
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\end{equation} |
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where the $\mathbf{r}_{ij}$ is the position vector between molecules |
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\emph{i} and \emph{j} with magnitude equal to the distance $r_ij$, and |
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$\boldsymbol{\Omega}_i$ and $\boldsymbol{\Omega}_j$ represent the |
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orientations of the respective molecules. The Lennard-Jones, dipole, |
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and sticky parts of the potential are giving by the following |
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equations, |
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\begin{equation} |
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u_{ij}^{LJ}(r_{ij}) = 4\epsilon \left[\left(\frac{\sigma}{r_{ij}}\right)^{12}-\left(\frac{\sigma}{r_{ij}}\right)^{6}\right], |
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\end{equation} |
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\begin{equation} |
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u_{ij}^{dp} = \frac{\boldsymbol{\mu}_i\cdot\boldsymbol{\mu}_j}{r_{ij}^3}-\frac{3(\boldsymbol{\mu}_i\cdot\mathbf{r}_{ij})(\boldsymbol{\mu}_j\cdot\mathbf{r}_{ij})}{r_{ij}^5}\ , |
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\end{equation} |
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\begin{equation} |
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\begin{split} |
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u_{ij}^{sp} |
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(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j) |
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&= |
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\frac{\nu_0}{2}[s(r_{ij})w(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j)\\ |
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& \quad \ + |
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s^\prime(r_{ij})w^\prime(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j)]\ , |
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\end{split} |
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\end{equation} |
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where $\boldsymbol{\mu}_i$ and $\boldsymbol{\mu}_j$ are the dipole |
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unit vectors of particles \emph{i} and \emph{j} with magnitude 2.35 D, |
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$\nu_0$ scales the strength of the overall sticky potential, $s$ and |
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$s^\prime$ are cubic switching functions. The $w$ and $w^\prime$ |
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functions take the following forms, |
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\begin{equation} |
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w(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j)=\sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij}, |
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\end{equation} |
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\begin{equation} |
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w^\prime(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j) = (\cos\theta_{ij}-0.6)^2(\cos\theta_{ij}+0.8)^2-w^0, |
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\end{equation} |
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where $w^0 = 0.07715$. The $w$ function is the tetrahedral attractive |
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term that promotes hydrogen bonding orientations within the first |
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solvation shell, and $w^\prime$ is a dipolar repulsion term that |
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repels unrealistic dipolar arrangements within the first solvation |
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shell. A more detailed description of the functional parts and |
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variables in this potential can be found in other |
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articles.\cite{liu96:new_model,chandra99:ssd_md} |
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|
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Since SSD is a one-site point dipole model, the force calculations are |
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simplified significantly from a computational standpoint, in that the |
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number of long-range interactions is dramatically reduced. In the |
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original Monte Carlo simulations using this model, Ichiye \emph{et |
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al.} reported a calculation speed up of up to an order of magnitude |
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over other comparable models while maintaining the structural behavior |
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of water.\cite{liu96:new_model} In the original molecular dynamics studies of |
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SSD, it was shown that it actually improves upon the prediction of |
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water's dynamical properties over TIP3P and SPC/E.\cite{chandra99:ssd_md} |
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|
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Recent constant pressure simulations revealed issues in the original |
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SSD model that led to lower than expected densities at all target |
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pressures.\cite{Ichiye03,Gezelter04} Reparameterizations of the |
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original SSD have resulted in improved density behavior, as well as |
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alterations in the water structure and transport behavior. {\sc oopse} is |
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easily modified to impliment these new potential parameter sets for |
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the derivative water models: SSD1, SSD/E, and SSD/RF. All of the |
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variable parameters are listed in the accompanying BASS file, and |
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these parameters simply need to be changed to the updated values. |
